Re: [gmx-users] Error in grompp minimization
On 6/10/13 8:51 PM, Souilem Safa wrote: Dear gromacs users, I'm trying to simulate a single molecule in cyclohexane. I made a box of my molecule using editconf command and next I solvate with cyclohexane using genbox command : genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro I did next a position restraint in the topolgy file and I tried to minimize, i got this fatal error: Fatal error: No such moleculetype CHX What could be the origin of this error. You probably forgot to #include the topology that introduces CHX as a valid [moleculetype]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in grompp minimization
Dear Justin, thank you for your reply. Yes, you are right , I have corrected it already and now it works well. Cheers, Safa On 11 June 2013 09:53, Justin Lemkul jalem...@vt.edu wrote: On 6/10/13 8:51 PM, Souilem Safa wrote: Dear gromacs users, I'm trying to simulate a single molecule in cyclohexane. I made a box of my molecule using editconf command and next I solvate with cyclohexane using genbox command : genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro I did next a position restraint in the topolgy file and I tried to minimize, i got this fatal error: Fatal error: No such moleculetype CHX What could be the origin of this error. You probably forgot to #include the topology that introduces CHX as a valid [moleculetype]. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error after grompp
Hello, Hi all, I need to do simulation which same as protein-ligand tutorial by Justin. The different is i'm using my protein and the ligand was zinc. I already follow everything in that tutorial and suddenly when i want to heat my protein by using the nvt.mdp there was an error state like below : Fatal error: Atom 410 in multiple T-Coupling groups (1 and 2) This means that atom no. 410 is defined in both the coupling groups which you have defined in the temperature coupling segment of your mdp file. Looking at your file it seems to me that the Zn atom is the culprit. In case the parameters for the Zn are being directly taken from the force field ions.itp file, then i think gromacs treats this as an ion and would automatically assigns to Water_and _ions group. Actually I do not understand what the error said even when i'm Google it to forum there was no one facing like mine..Here i put together my topology and the nvt.mdp. Hope you can give me some idea that i cant see. Another question,why is in the nvt.mdp at the temperature coupling there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u explain it why? this has been explained quite clearly in the gromacs manual. In essence, defining different coupling groups allows control over the temperature of the Groups especially protein and water which otherwise have been seen to differ in the temperature attained by a large degree. Cheers Abhishek Acharya Structural and Computational Biology Lab IIt Kanpur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error during grompp run
On Wed, Mar 20, 2013 at 2:30 AM, Kshatresh Dutta Dubey kshatr...@ymail.comwrote: Dear Justin, I checked for it several times and I am quite sure there is no typo error, permission problem and location of posre_Protein.itp file. Even, I run same job on different machines from beginning and I found same type of error. Without seeing the relevant topology snippet, listing of files in the working directory (ls -l), and the grompp command invoked, there's no way for anyone to help you. This should be a relatively easy fix. The fact that it does not work on multiple machines indicates there is indeed a problem with either the file name or the manner in which it is included in the topology. What is posre_Protein.itp? What it written by pdb2gmx with a nonstandard name or was it something you created? -Justin -- *From:* Justin Lemkul jalem...@vt.edu *To:* Kshatresh Dutta Dubey kshatr...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, March 19, 2013 10:48 PM *Subject:* Re: [gmx-users] Error during grompp run On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey kshatr...@ymail.com wrote: Dear Users I am using groamcs 4.4.4 and when I run grompp during equilibration process, it closes with error Fatal error:Topology include file posre_Protein.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; However, I found Topology include file posre_Protein.itp in current directory. I am able to successfully run previous grompp during minimization, but I am facing this problem during equilibration only. Please help me to get rid of this issue. I welcome all suggestions. If grompp says it's not there, it's not there. Check carefully for typos in file names or #include statements as well as read permissions on the file itself. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error during grompp run
On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey kshatr...@ymail.com wrote: Dear Users I am using groamcs 4.4.4 and when I run grompp during equilibration process, it closes with error Fatal error:Topology include file posre_Protein.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; However, I found Topology include file posre_Protein.itp in current directory. I am able to successfully run previous grompp during minimization, but I am facing this problem during equilibration only. Please help me to get rid of this issue. I welcome all suggestions. If grompp says it's not there, it's not there. Check carefully for typos in file names or #include statements as well as read permissions on the file itself. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp
On 10/7/12 8:42 PM, Nur Syafiqah Abdul Ghani wrote: Dear All, Fatal error: number of coordinates in coordinate file (prot_wtr_solv.gro, 18031) does not match topology (control.top, 16650) It happen when i started to minimize it by using the command grompp -v -f minim_first.mdp -p control.top -c prot_wtr_solv.gro -o minim_prot.tpr -zero When i open the control.top and the prot_wtr_solv.gro file and i startet to calculate the missing atom is about 1381 which is for my DRG molecule.. I already edit and put the topology like below : ; Include topology for DRG #include solvent.itp [ system ] ; Name ALZHEIMER'S DISEASE AMYLOID in water [ molecules ] ; Compound#mols Protein_chain_A 1 DRG1381 SOL 350 Can you guys please explain it to me why this happened..Its still cant be minimize it yet.. The answer to this error is always the same. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology You need to keep better track of the molecules in your system and adjust the topology accordingly. When dealing with complex systems, you must do your own bookkeeping. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? Elie Date: Fri, 5 Oct 2012 13:06:34 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/5/12 1:00 PM, Elie M wrote: I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save. 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed). Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp? Whatever changes you made were apparently ineffectual. You need to make sure that you are adding parameters in the correct directives (i.e. bonds in [bondtypes], angles in [angletypes], etc). Without seeing exactly what you've done, all I can say is that whatever you did wasn't correct. The approach is theoretically sound, though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? Elie Date: Sat, 6 Oct 2012 13:26:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/6/12 1:57 PM, Elie M wrote: Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? In principle, I don't think it should matter, but it's something you can check yourself in less time than it takes to send an email :) -Justin Elie Date: Sat, 6 Oct 2012 13:26:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Yeah sorry about that. i thought about it at the moment I was sending the e-mail..The problem I am so desperate about getting all files correct to minimize my polymer. It has really taken a long time. Anyhow you were right. Switching the order did not do anything; the error is still there. Now it is a bit weird because the bond is there in the file then why it cannot find it? Any suggestions? Elie Date: Sat, 6 Oct 2012 13:59:10 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:57 PM, Elie M wrote: Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? In principle, I don't think it should matter, but it's something you can check yourself in less time than it takes to send an email :) -Justin Elie Date: Sat, 6 Oct 2012 13:26:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/6/12 1:18 PM, Elie M wrote: This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to all-atom S: thiophenol (HS is #204); the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? It may be a matter of the order of the atoms. SH is indeed sulfur (you can tell by the mass in atomtypes.atp and the fact that the first letter is S). The corresponding H atom is HS, so that's not the problem. The parameters for this bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 version): CASH 10.17400 209200.0 ; wlj -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/6/12 2:30 PM, Elie M wrote: Yeah sorry about that. i thought about it at the moment I was sending the e-mail..The problem I am so desperate about getting all files correct to minimize my polymer. It has really taken a long time. Anyhow you were right. Switching the order did not do anything; the error is still there. Now it is a bit weird because the bond is there in the file then why it cannot find it? Any suggestions? I will attempt to debug this. Please send me (off-list): 1. Your coordinate file 2. Your topology 3. The .mdp file you are using 4. The force field files -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save. 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed). Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp? Thanks Elie Date: Thu, 4 Oct 2012 21:25:29 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 5:56 PM, Elie M wrote: I guess the first parameter of each pair is easy to find. what about kb? k theta?. kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help. Bonded parameters are generally based on vibrational spectra and X-ray data. For OPLS, the bonded parameters were originally taken from an AMBER parameter set in the mid-1980's and have some terms have subsequently been revised over time. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/5/12 1:00 PM, Elie M wrote: I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save. 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed). Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp? Whatever changes you made were apparently ineffectual. You need to make sure that you are adding parameters in the correct directives (i.e. bonds in [bondtypes], angles in [angletypes], etc). Without seeing exactly what you've done, all I can say is that whatever you did wasn't correct. The approach is theoretically sound, though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? Thank you. Elie Date: Wed, 3 Oct 2012 22:09:02 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/3/12 7:48 PM, Elie M wrote: Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include ffoplsaamod.itp[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ;), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include ffoplsaanb.itp#include ffoplsaabon.itp where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ; and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum It seems like the format of whatever files you're using is horribly broken. I would recommend starting over and not making any adjustments to any files (removing lines, changing contents, adding comments, etc) unless you know exactly what you're doing. For example, the presence of '\par' in ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text editor). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 10:12 AM, Elie M wrote: Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters You should inspect ffoplsaabon.itp to see what is on these lines. It is odd that grompp would complain about standard force field files if they have not been changed. and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds that are not parameterized in the chosen force field) you need to add them either in ffbonded.itp (potentially dangerous, given the previous posts) or directly in the topology (probably safer). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ; one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 1 47 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? Elie Date: Thu, 4 Oct 2012 10:26:04 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 10:12 AM, Elie M wrote: Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters You should inspect ffoplsaabon.itp to see what is on these lines. It is odd that grompp would complain about standard force field files if they have not been changed. and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds that are not parameterized in the chosen force field) you need to add them either in ffbonded.itp (potentially dangerous, given the previous posts) or directly in the topology (probably safer). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 12:13 PM, Elie M wrote: Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ; one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 147 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? The error message means that no suitable parameters exist in the force field for the bond that occurs between those atoms. You either need to parameterize the problematic bond(s) yourself or obtain parameters from some other reliable source. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? Thank you very much Elie Date: Thu, 4 Oct 2012 12:25:48 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 12:13 PM, Elie M wrote: Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ; one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 147 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? The error message means that no suitable parameters exist in the force field for the bond that occurs between those atoms. You either need to parameterize the problematic bond(s) yourself or obtain parameters from some other reliable source. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 4:22 PM, Elie M wrote: I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the You will have to calculate reasonable values in some way, yes. parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? All of this is in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
I guess the first parameter of each pair is easy to find. what about kb? k theta?. kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help. Elie Date: Thu, 4 Oct 2012 16:25:35 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 4:22 PM, Elie M wrote: I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the You will have to calculate reasonable values in some way, yes. parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? All of this is in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 5:56 PM, Elie M wrote: I guess the first parameter of each pair is easy to find. what about kb? k theta?. kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help. Bonded parameters are generally based on vibrational spectra and X-ray data. For OPLS, the bonded parameters were originally taken from an AMBER parameter set in the mid-1980's and have some terms have subsequently been revised over time. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an #include command# referring to the .itp file. so my top file now just looks like that: ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include ffoplsaamod.itp and my foplsaamod.itp has the info that was present in .top file i.e: [ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. Thank you Elie . Date: Tue, 2 Oct 2012 03:56:28 + . From: emanuel.bi...@monash.edu . Subject: RE: [gmx-users] Error with grompp To: gmx-users@gromacs.org Hi Elie, Your email is a bit confusing but I will try to give you some idea as per my understanding of your email. If you want to use top and itp files separately, you should put all the info (molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and you should use # include your itp file.itp in your top file. No atom, bond, pair etc in your top file. Just like you include your water type (spc/tip4) you should include the itp. And top of that you should put the right number of molecules in the right order in your top file at the (molecules) section. Hope that might give you some help. Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Elie M Sent: Tuesday, 2 October 2012 1:39 PM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Error with grompp I am a bit confused..I am getting different errors though similar in goal. The error this time is: Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atomsLet me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an ffoplsaamod.itp, i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files : ffoplsaanb.itp and ffoplsaabon.itp, I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called
Re: [gmx-users] Error with grompp
On 10/3/12 10:03 AM, Elie M wrote: Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an #include command# referring to the .itp file. so my top file now just looks like that: That doesn't really make any sense. You've chopped out the information for your molecule from the topology that g_x2top wrote, then simply re-included that information? The output of g_x2top should be a functional topology; you should not have to adjust it. If you need this topology to be an .itp file, i.e. as a ligand in some other .top, then you only need to make small adjustments. See the following: http://www.gromacs.org/Documentation/File_Formats/.itp_File ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include ffoplsaamod.itp and my foplsaamod.itp has the info that was present in .top file i.e: [ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 I don't know whether it is your email client or the topology itself, but the seemingly random line breaks make these posts very difficult to read. [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. A topology follows a defined structure that must be observed. The hierarchy is described in the manual, but can be distilled into the following requirements: 1. You must #include a force field that defines all default elements (i.e. a [defaults] directive) that govern how the force field operates. 2. You must #include the nonbonded and bonded parameters for that force field, in that order. Bonded parameters are assigned based on atom types, which must be declared first in order to be used. 3. After all force field-level parameters (items 1 and 2), you can introduce molecules that use these parameters. This is the point where you can proceed to [atoms], [bonds], etc for a particular molecule. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include ffoplsaamod.itp[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ;), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include ffoplsaanb.itp#include ffoplsaabon.itp where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ; and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum Elie Date: Wed, 3 Oct 2012 10:15:07 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/3/12 10:03 AM, Elie M wrote: Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an #include command# referring to the .itp file. so my top file now just looks like that: That doesn't really make any sense. You've chopped out the information for your molecule from the topology that g_x2top wrote, then simply re-included that information? The output of g_x2top should be a functional topology; you should not have to adjust it. If you need this topology to be an .itp file, i.e. as a ligand in some other .top, then you only need to make small adjustments. See the following: http://www.gromacs.org/Documentation/File_Formats/.itp_File ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include ffoplsaamod.itp and my foplsaamod.itp has the info that was present in .top file i.e: [ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 I don't know whether it is your email client or the topology itself, but the seemingly random line breaks make these posts very difficult to read. [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. A topology follows a defined structure that must be observed. The hierarchy is described in the manual, but can be distilled into the following requirements: 1. You must #include a force field that defines all default elements (i.e. a [defaults
Re: [gmx-users] Error with grompp
On 10/3/12 7:48 PM, Elie M wrote: Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include ffoplsaamod.itp[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ;), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include ffoplsaanb.itp#include ffoplsaabon.itp where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ; and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum It seems like the format of whatever files you're using is horribly broken. I would recommend starting over and not making any adjustments to any files (removing lines, changing contents, adding comments, etc) unless you know exactly what you're doing. For example, the presence of '\par' in ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text editor). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp
On 10/2/12 11:26 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But grompp (before minimization of system_inflated.gro) giving error like this.. Fatal error: Atomtype LC3 not found Actually what changes I should do on the system topology, before grompp? I found that atomtype LC3 is found in my dppc.itp file. If you're following my tutorial, then you have skipped a step or not completed the force field modifications. Go back and ensure that ffnonbonded.itp has been modified correctly to include the atom types and parameters from lipid.itp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Thanks for your time and help as always. I will see what I can do about that. Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
I am a bit confused..I am getting different errors though similar in goal. The error this time is: Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atomsLet me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an ffoplsaamod.itp, i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files : ffoplsaanb.itp and ffoplsaabon.itp, I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Hi Elie, Your email is a bit confusing but I will try to give you some idea as per my understanding of your email. If you want to use top and itp files separately, you should put all the info (molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and you should use # include your itp file.itp in your top file. No atom, bond, pair etc in your top file. Just like you include your water type (spc/tip4) you should include the itp. And top of that you should put the right number of molecules in the right order in your top file at the (molecules) section. Hope that might give you some help. Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Elie M Sent: Tuesday, 2 October 2012 1:39 PM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Error with grompp I am a bit confused..I am getting different errors though similar in goal. The error this time is: Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atomsLet me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an ffoplsaamod.itp, i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files : ffoplsaanb.itp and ffoplsaabon.itp, I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp
Hi Justin, thank you very much for your help!! On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. Now I tried it with two different restraint .itp files. One for the protein and one for the dummy atoms. But still it doesn't work. Now the error is: [ file posre_memb.itp, line 5 ]: Atom index (4942) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. But I think I included it the right way: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp #ifdef POSRES #include posre_memb.itp #endif In my coordiate file the difference between them look like this: 313LEU HD23 4938 3.813 4.505 3.308 313LEU C 4939 3.435 4.335 3.190 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 314DUMDUM 4943 1.996 2.371 6.271 314DUMDUM 4944 1.996 2.471 6.171 314DUMDUM 4945 1.996 2.471 6.271 my restraint file for the protein looks like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 41 1000 1000 1000 71 1000 1000 1000 101 1000 1000 1000 131 1000 1000 1000 and my restraint file for the dummy atoms look like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 49421 1000 1000 1000 49431 1000 1000 1000 49441 1000 1000 1000 49451 1000 1000 1000 What is wrong? Atom numbering is done per [moleculetype] and has nothing to do with the atom numbers in the coordinate file. If you have a one-atom dummy [moleculetype], then the only valid content of posre_memb.itp is: [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp
Hi Justin, thank you for your answer. Now I tried it with two different restraint .itp files. One for the protein and one for the dummy atoms. But still it doesn't work. Now the error is: [ file posre_memb.itp, line 5 ]: Atom index (4942) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. But I think I included it the right way: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp #ifdef POSRES #include posre_memb.itp #endif In my coordiate file the difference between them look like this: 313LEU HD23 4938 3.813 4.505 3.308 313LEU C 4939 3.435 4.335 3.190 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 314DUMDUM 4943 1.996 2.371 6.271 314DUMDUM 4944 1.996 2.471 6.171 314DUMDUM 4945 1.996 2.471 6.271 my restraint file for the protein looks like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 41 1000 1000 1000 71 1000 1000 1000 101 1000 1000 1000 131 1000 1000 1000 and my restraint file for the dummy atoms look like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 49421 1000 1000 1000 49431 1000 1000 1000 49441 1000 1000 1000 49451 1000 1000 1000 What is wrong? Thank you for your help!! Eva On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want do to an energy minimization and simulation with position restraints. Additionally to the protein I have a membrane around my protein which I also ant to fix. If I won't fix it, it is in the whole box after the minimization and simulation but not around my protein. Since I only want the hydrogen atoms to be flexible I use the second option protein-h when I was asked by genrestr. This makes that the whole protein including the membrane of dummy atoms is fix. But when I want to use grompp I get the error: Atom index (4942) in position_restraints out of bounds (1-4941). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. The first 4941 atoms are of the real protein without the membrane and after this the membrane starts: 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 315DUMDUM 4943 1.996 2.371 6.271 316DUMDUM 4944 1.996 2.471 6.171 When I remove the restriction of the DUM atoms I don't get the error but that is not what I want. Can you please tell me how I can fix the membrane? You need a separate position restraint .itp file. As the error message states, position restraints are only applicable per [moleculetype]. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] error in grompp
On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. Now I tried it with two different restraint .itp files. One for the protein and one for the dummy atoms. But still it doesn't work. Now the error is: [ file posre_memb.itp, line 5 ]: Atom index (4942) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. But I think I included it the right way: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp #ifdef POSRES #include posre_memb.itp #endif In my coordiate file the difference between them look like this: 313LEU HD23 4938 3.813 4.505 3.308 313LEU C 4939 3.435 4.335 3.190 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 314DUMDUM 4943 1.996 2.371 6.271 314DUMDUM 4944 1.996 2.471 6.171 314DUMDUM 4945 1.996 2.471 6.271 my restraint file for the protein looks like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 41 1000 1000 1000 71 1000 1000 1000 101 1000 1000 1000 131 1000 1000 1000 and my restraint file for the dummy atoms look like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 49421 1000 1000 1000 49431 1000 1000 1000 49441 1000 1000 1000 49451 1000 1000 1000 What is wrong? Atom numbering is done per [moleculetype] and has nothing to do with the atom numbers in the coordinate file. If you have a one-atom dummy [moleculetype], then the only valid content of posre_memb.itp is: [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp
On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want do to an energy minimization and simulation with position restraints. Additionally to the protein I have a membrane around my protein which I also ant to fix. If I won't fix it, it is in the whole box after the minimization and simulation but not around my protein. Since I only want the hydrogen atoms to be flexible I use the second option protein-h when I was asked by genrestr. This makes that the whole protein including the membrane of dummy atoms is fix. But when I want to use grompp I get the error: Atom index (4942) in position_restraints out of bounds (1-4941). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. The first 4941 atoms are of the real protein without the membrane and after this the membrane starts: 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 315DUMDUM 4943 1.996 2.371 6.271 316DUMDUM 4944 1.996 2.471 6.171 When I remove the restriction of the DUM atoms I don't get the error but that is not what I want. Can you please tell me how I can fix the membrane? You need a separate position restraint .itp file. As the error message states, position restraints are only applicable per [moleculetype]. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. I also have the tip4p.gro and tip5p.gro file. Can I also use them? On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
My topology file looks like this: 4924 4940 4939 4941 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13486 So I don't think that the #include of the itp3p is wrong. I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. I already included the dummy atoms in the files atomtypes.atp, ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. So I was puzzled that it didn't know the atomtype dum during the grompp run. On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post
Re: [gmx-users] error with grompp
On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: My topology file looks like this: 4924 4940 4939 4941 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13486 So I don't think that the #include of the itp3p is wrong. OK, and what's inside it? I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. Well, this is non-standard, but I can't see how it would matter. I already included the dummy atoms in the files atomtypes.atp, ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. So I was puzzled that it didn't know the atomtype dum during the grompp run. So what purpose is being served by that dum.itp? Mark On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages
Re: [gmx-users] error with grompp
Content of the ipt3p.itp file: ; This file is for backward compatibility only. ; Please directly include the tip3p.itp file from your force field directory. #ifdef _FF_GROMACS #include gmx.ff/tip3p.itp #endif #ifdef _FF_GROMOS96 #include gromos43a1.ff/tip3p.itp #endif #ifdef _FF_OPLS #include oplsaa.ff/tip3p.itp #endif I additionally included the dum.itp file since grompp seems not to read the changes I made in the several files. I still get the error that the atomtype DUM is not known. The dummy atoms in the .gro file look like this: 314DUMDUM 4942 4.007 4.409 4.090 my changes are: atomtypes.atp: DU 1.0 ; Dummy atom for the membrane DUM1.0 ffnonbonded.itp: DU 0 1. 0. A 0.0e+00 0.0e+00 DUM 0 1. 0. A 0.0e+00 0.0e+00 aminoacids.rtp: [ DUM ] [ atoms ] DUM DU 0.001 residuetypes.dat: DUM Protein vdwradii.dat: ??? D 0.15 Is there any problem why it should not read my changes? On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: My topology file looks like this: 4924 4940 4939 4941 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13486 So I don't think that the #include of the itp3p is wrong. OK, and what's inside it? I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. Well, this is non-standard, but I can't see how it would matter. I already included the dummy atoms in the files atomtypes.atp, ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. So I was puzzled that it didn't know the atomtype dum during the grompp run. So what purpose is being served by that dum.itp? Mark On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of
Re: [gmx-users] error with grompp
On 07/02/2012 07:00 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Content of the ipt3p.itp file: ; This file is for backward compatibility only. ; Please directly include the tip3p.itp file from your force field directory. #ifdef _FF_GROMACS #include gmx.ff/tip3p.itp #endif #ifdef _FF_GROMOS96 #include gromos43a1.ff/tip3p.itp #endif #ifdef _FF_OPLS #include oplsaa.ff/tip3p.itp #endif amber03.ff/tip3p.itp has never contained that - you've taken it from the top-level $GMXLIB directory, from which it can't be moved, and can't work with AMBER force fields. This completely explains your symptoms. Since none of those _FF_* are defined, there's no water-related content in your .top file. However you have constructed your amber03.ff is wrong. I'd strongly suggest getting a new copy of amber03.ff (possibly after upgrading to GROMACS 4.5.5) and starting again. The diff tool may be your friend here. I additionally included the dum.itp file since grompp seems not to read the changes I made in the several files. Then you've done something wrong. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field contains the kind of procedure you need to follow. Mark I still get the error that the atomtype DUM is not known. The dummy atoms in the .gro file look like this: 314DUMDUM 4942 4.007 4.409 4.090 my changes are: atomtypes.atp: DU 1.0 ; Dummy atom for the membrane DUM1.0 ffnonbonded.itp: DU 0 1. 0. A 0.0e+00 0.0e+00 DUM 0 1. 0. A 0.0e+00 0.0e+00 aminoacids.rtp: [ DUM ] [ atoms ] DUM DU 0.001 residuetypes.dat: DUM Protein vdwradii.dat: ??? D 0.15 Is there any problem why it should not read my changes? On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: My topology file looks like this: 4924 4940 4939 4941 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13486 So I don't think that the #include of the itp3p is wrong. OK, and what's inside it? I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. Well, this is non-standard, but I can't see how it would matter. I already included the dummy atoms in the files atomtypes.atp, ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. So I was puzzled that it didn't know the atomtype dum during the grompp run. So what purpose is being served by that dum.itp? Mark On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA
Re: [gmx-users] error with grompp
Ah, okey thank you. I will try to install it again. I made the changes of the files exactly as it is descriped on the site you wrote me. I send you in the last mail my changes in the files. Do you think they are okey? I was not completely sure about atomtype and residuetype and so on. Best, Eva On 07/02/2012 07:00 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Content of the ipt3p.itp file: ; This file is for backward compatibility only. ; Please directly include the tip3p.itp file from your force field directory. #ifdef _FF_GROMACS #include gmx.ff/tip3p.itp #endif #ifdef _FF_GROMOS96 #include gromos43a1.ff/tip3p.itp #endif #ifdef _FF_OPLS #include oplsaa.ff/tip3p.itp #endif amber03.ff/tip3p.itp has never contained that - you've taken it from the top-level $GMXLIB directory, from which it can't be moved, and can't work with AMBER force fields. This completely explains your symptoms. Since none of those _FF_* are defined, there's no water-related content in your .top file. However you have constructed your amber03.ff is wrong. I'd strongly suggest getting a new copy of amber03.ff (possibly after upgrading to GROMACS 4.5.5) and starting again. The diff tool may be your friend here. I additionally included the dum.itp file since grompp seems not to read the changes I made in the several files. Then you've done something wrong. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field contains the kind of procedure you need to follow. Mark I still get the error that the atomtype DUM is not known. The dummy atoms in the .gro file look like this: 314DUMDUM 4942 4.007 4.409 4.090 my changes are: atomtypes.atp: DU 1.0 ; Dummy atom for the membrane DUM1.0 ffnonbonded.itp: DU 0 1. 0. A 0.0e+00 0.0e+00 DUM 0 1. 0. A 0.0e+00 0.0e+00 aminoacids.rtp: [ DUM ] [ atoms ] DUM DU 0.001 residuetypes.dat: DUM Protein vdwradii.dat: ??? D 0.15 Is there any problem why it should not read my changes? On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: My topology file looks like this: 4924 4940 4939 4941 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13486 So I don't think that the #include of the itp3p is wrong. OK, and what's inside it? I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. Well, this is non-standard, but I can't see how it would matter. I already included the dummy atoms in the files atomtypes.atp, ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. So I was puzzled that it didn't know the atomtype dum during the grompp run. So what purpose is being served by that dum.itp? Mark On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and
Re: [gmx-users] error with grompp
On 07/02/2012 10:07 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah, okey thank you. I will try to install it again. I made the changes of the files exactly as it is descriped on the site you wrote me. I send you in the last mail my changes in the files. Do you think they are okey? I was not completely sure about atomtype and residuetype and so on. They look plausible, but the proof is in whether it works. Mark Best, Eva On 07/02/2012 07:00 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Content of the ipt3p.itp file: ; This file is for backward compatibility only. ; Please directly include the tip3p.itp file from your force field directory. #ifdef _FF_GROMACS #include gmx.ff/tip3p.itp #endif #ifdef _FF_GROMOS96 #include gromos43a1.ff/tip3p.itp #endif #ifdef _FF_OPLS #include oplsaa.ff/tip3p.itp #endif amber03.ff/tip3p.itp has never contained that - you've taken it from the top-level $GMXLIB directory, from which it can't be moved, and can't work with AMBER force fields. This completely explains your symptoms. Since none of those _FF_* are defined, there's no water-related content in your .top file. However you have constructed your amber03.ff is wrong. I'd strongly suggest getting a new copy of amber03.ff (possibly after upgrading to GROMACS 4.5.5) and starting again. The diff tool may be your friend here. I additionally included the dum.itp file since grompp seems not to read the changes I made in the several files. Then you've done something wrong. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field contains the kind of procedure you need to follow. Mark I still get the error that the atomtype DUM is not known. The dummy atoms in the .gro file look like this: 314DUMDUM 4942 4.007 4.409 4.090 my changes are: atomtypes.atp: DU 1.0 ; Dummy atom for the membrane DUM1.0 ffnonbonded.itp: DU 0 1. 0. A 0.0e+00 0.0e+00 DUM 0 1. 0. A 0.0e+00 0.0e+00 aminoacids.rtp: [ DUM ] [ atoms ] DUM DU 0.001 residuetypes.dat: DUM Protein vdwradii.dat: ??? D 0.15 Is there any problem why it should not read my changes? On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: My topology file looks like this: 4924 4940 4939 4941 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/dum.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13486 So I don't think that the #include of the itp3p is wrong. OK, and what's inside it? I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. Well, this is non-standard, but I can't see how it would matter. I already included the dummy atoms in the files atomtypes.atp, ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. So I was puzzled that it didn't know the atomtype dum during the grompp run. So what purpose is being served by that dum.itp? Mark On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey thank you. But shell I also #include amber03.ff/spc.itp Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. The only thing that makes sense is to use only amber03/tip3p.itp, like Justin said. It defines the SOL [moleculetype], so your observations do not seem consistent with #including such a file. Your .top fragment suggests you're #including them at quite different points, and maybe the point at with you #include tip3p is inappropriate (e.g. inside an #ifdef). Mark But in one of the last mails Justin wrote that: You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file I also have the tip4p.gro and tip5p.gro file. Can I also use them? No. Mark On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and
Re: [gmx-users] error with grompp
Hi, Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections. Cheers, Shima From: reising...@rostlab.informatik.tu-muenchen.de reising...@rostlab.informatik.tu-muenchen.de To: gmx-users@gromacs.org Sent: Friday, June 29, 2012 5:24 PM Subject: [gmx-users] error with grompp Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound #mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. Well, it is a correct outcome of genion, but it is incorrect usage. From genion -h: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead! -Justin But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 6/29/12 9:04 AM, Shima Arasteh wrote: Hi, Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections. Incorrect order will lead to a series of non-matching atom names in the grompp output. In this case, the error comes from incorrect usage of genion (see my previous post). -Justin Cheers, Shima From: reising...@rostlab.informatik.tu-muenchen.de reising...@rostlab.informatik.tu-muenchen.de To: gmx-users@gromacs.org Sent: Friday, June 29, 2012 5:24 PM Subject: [gmx-users] error with grompp Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
So just entering the -pname NA and -nname CL ! Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, June 29, 2012 5:36 PM Subject: Re: [gmx-users] error with grompp On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound #mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. Well, it is a correct outcome of genion, but it is incorrect usage. From genion -h: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead! -Justin But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
Hi Justin, thank you for your answer. So you mean that I should only name NA and CL like this: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA -nname CL But when I now want to run the alraedy mentioned grompp command I get the error: No such moleculetype NA Can this be because of the wrong including order? I included everything this order: ; Include forcefield parameters #include amber03.ff/forcefield.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp Bests Eva On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. Well, it is a correct outcome of genion, but it is incorrect usage. From genion -h: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead! -Justin But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
Thank you for your answer. I tried it only with NA and CL and it also didn't work. Now I have the same error with NA Bests Eva Hi, Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections. Cheers, Shima From: reising...@rostlab.informatik.tu-muenchen.de reising...@rostlab.informatik.tu-muenchen.de To: gmx-users@gromacs.org Sent: Friday, June 29, 2012 5:24 PM Subject: [gmx-users] error with grompp Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound #mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 6/29/12 9:18 AM, Shima Arasteh wrote: So just entering the -pname NA and -nname CL ! Precisely, as genion -h instructs. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 6/29/12 9:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. So you mean that I should only name NA and CL like this: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA -nname CL This is a correct command. But when I now want to run the alraedy mentioned grompp command I get the error: No such moleculetype NA What does your [molecules] directive specify? Have you cleaned up the topology from the prior (incorrect) invocation of genion/grompp? Can this be because of the wrong including order? I included everything this order: The order of #include statements is irrelevant. The only order that matters is in [molecules], which must match the contents of the coordinate file. -Justin ; Include forcefield parameters #include amber03.ff/forcefield.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp Bests Eva On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. Well, it is a correct outcome of genion, but it is incorrect usage. From genion -h: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead! -Justin But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 Bests, Eva On 6/29/12 9:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. So you mean that I should only name NA and CL like this: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA -nname CL This is a correct command. But when I now want to run the alraedy mentioned grompp command I get the error: No such moleculetype NA What does your [molecules] directive specify? Have you cleaned up the topology from the prior (incorrect) invocation of genion/grompp? Can this be because of the wrong including order? I included everything this order: The order of #include statements is irrelevant. The only order that matters is in [molecules], which must match the contents of the coordinate file. -Justin ; Include forcefield parameters #include amber03.ff/forcefield.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp Bests Eva On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I added ions to the solvent around my structure with the command: genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. Well, it is a correct outcome of genion, but it is incorrect usage. From genion -h: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead! -Justin But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2logErr 1logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include amber03.ff/ions.itp What is wrong here? Best Eva -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error with grompp
On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include amber03.ff/tip3p.itp ; Include topology for ions #include amber03.ff/ions.itp #include amber03.ff/spc.itp #include amber03.ff/dum.itp You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology
On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology
Hi Justin, thank you for your answer. Now it worked and I could do the minimization. But now I have the same problem again but now the difference is 630. So what I did is that I ran the minimization and everything worked. And than I used the perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat command of the tutorial and now I got the error: number of coordinates in coordinate file (system_shrink1.gro, 9220) does not match topology (topol.top, 9850) But I changed nothing at the topology file. Bests, Eva On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology
Got it already. Thank you!! On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp run
On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, I want to do a MD simulation in vacuum. So don't turn on implicit solvent. So first I wanted to prepare the files for that with grompp. But there I got the error that With GBSA implicit solvent, rgbradii must be equal to rlist But the 2 values are the same in my .mdp file. Can you please show me where the failure is? define = -DPOSRES integrator = md emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = simple rgbradii= 0 rlist = 0 coulombtype = cutoff vdwtype = cutoff These are misspelled. See manual 7.3.9 for how to simulate without cut-offs. Mark rcoulomb= 0 rvdw= 0 pbc = no epsilon_rf = 0 implicit_solvent= GBSA gb_algorithm= HCT gb_epsilon_solvent = 78.3 nstxout = 1 nstfout = 1 nstvout = 1 nstxtcout = 1 nstlog = 1 Thank you, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp run
On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, I want to do a MD simulation in vacuum. So don't turn on implicit solvent. Sorry, my fault. I want to do it in implicit solvent. So first I wanted to prepare the files for that with grompp. But there I got the error that With GBSA implicit solvent, rgbradii must be equal to rlist But the 2 values are the same in my .mdp file. Can you please show me where the failure is? define = -DPOSRES integrator = md emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = simple rgbradii= 0 rlist = 0 coulombtype = cutoff vdwtype = cutoff These are misspelled. See manual 7.3.9 for how to simulate without cut-offs. Mark rcoulomb= 0 rvdw= 0 pbc = no epsilon_rf = 0 implicit_solvent= GBSA gb_algorithm= HCT gb_epsilon_solvent = 78.3 nstxout = 1 nstfout = 1 nstvout = 1 nstxtcout = 1 nstlog = 1 Thank you, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in grompp steps of position restrained
On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in grompp steps of position restrained
Dear Mark, Thanks for mail. you mean I need to define in mdp file?. Can you please guide me how to do that. Thanks. On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --**- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in grompp steps of position restrained
On 8/06/2012 12:34 PM, Malai wrote: Dear Mark, Thanks for mail. you mean I need to define in mdp file?. No. Using one of the two ways I suggested earlier depend what you're actually trying to do, but since your intention in using the CA group is unknown to us, you're preventing yourself getting specific help. Can you please guide me how to do that. Thanks. http://www.gromacs.org/Documentation/File_Formats/Index_File Mark On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in grompp steps of position restrained
Dear MARK, Dear Mark, Thanks for mail. you mean I need to define in mdp file?. No. Using one of the two ways I suggested earlier depend what you're actually trying to do, but since your intention in using the CA group is unknown to us, you're preventing yourself getting specific help. The error is CA index file. So my intention is to use CA group and avoid the error. please suggest me how to use grompp or make CA index file for grompp in position restrained step. Can you please guide me how to do that. Thanks. http://www.gromacs.org/Documentation/File_Formats/Index_File so i need to make index files for CA atoms of protein using make_ndx for CA. can you please explain how to make index file for CA using make_ndx. Thanks for help. Mark On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/06/2012 12:23 PM, Malai wrote: Hi, After Successfully neutralizing and sd minimization of the system, I got the below error when I try the grompp for position restrained step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr Any help will be highly appreciated. Many thanks. Error message: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group CA not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your .mdp file referred to a group for which grompp could find no definition. Choose a better group or make a definition. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in grompp
Serena Leone wrote: Hi all I am trying to model a sulfated octasaccharide. I retrieved the topology files from prodrg and I fixed them. The same procedure on a the monosaccharide unit of the oligosaccharide I'm going to run worked smoothly. After solvating the molecule, I try to pre-process it and I obtain the following error: -- Generated 279 of the 1225 non-bonded parameter combinations WARNING 1 [file GI.top, line 993]: Too few parameters on line (source file toppush.c, line 1168) processing coordinates... --- Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 469 Fatal error: number of coordinates in coordinate file (GI_wb.gro, 17431) does not match topology (GI.top, 0) According to the wiki, the fact that no atom is recognized in the top points to an incorrect location of the path for the cpp in the mdp, but this is not the case (i double checked, plus this is exactly the same mdp file that i used for other runs and that worked fine...). I also checked for mispellings of atoms and residues names in the top, but everything apparently fits. Do you have any idea of what else may cause this behavior? One can only blame cpp if the error messages show up as they appear on the wiki, but the output you've shown does not indicate that as a problem. If this is not the case, there are several other possibilities. Usually it's something simple, like a type in an #include line, or including the relevant .itp files in the wrong order, or something else less obvious. It looks like there is another problem: Too few parameters on line... so I would explore that error to see if that is causing some failure in the grompp process. -Justin Thanks a lot Cheers, Serena -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error during grompp
Yulia Einav wrote: Dear Gromacs users, During my last simulation of 2 ns a part of a protein moved out of the water box. When I've tried to proceed to the next 2 ns I've got the folowing message during grompp: Fatal error: number of coordinates in coordinate file (wt_md2_egf4.gro, 17346) does not match topology (topol.top, 0) there is something wrong in your topology. check manual chapter 5 and error messages from grompp. Furthemore the same part of the protein always move out of the box in different simulations. Is there any way to prevent the moving? How do I continue the simulation from this point? Thank you for your help, Yulia Yulia Einav Ph.D. Mathematical Biology Unit Department of Applied Mathematics Faculty of Sciences, H.I.T. 52 Golomb Str. POB 305, Holon 58102, Israel. Tel. 972-3-5026769, Fax. 972-3-5026619. E-mail: [EMAIL PROTECTED], Web: http://www.hit.ac.il http://www.hit.ac.il/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error during grompp
Running out of box is common and it actually doesn't because of PBC. You may just continue the simulation For this fatal error, you shall refer to how you have created the first tpr file: which top file you have used. On 7/17/2007 5:39 PM, Yulia Einav wrote: Dear Gromacs users, During my last simulation of 2 ns a part of a protein moved out of the water box. When I've tried to proceed to the next 2 ns I've got the folowing message during grompp: Fatal error: number of coordinates in coordinate file (wt_md2_egf4.gro, 17346) does not match topology (topol.top, 0) Furthemore the same part of the protein always move out of the box in different simulations. Is there any way to prevent the moving? How do I continue the simulation from this point? Thank you for your help, Yulia Yulia Einav Ph.D. Mathematical Biology Unit Department of Applied Mathematics Faculty of Sciences, H.I.T. 52 Golomb Str. POB 305, Holon 58102, Israel. Tel. 972-3-5026769, Fax. 972-3-5026619. E-mail: [EMAIL PROTECTED], Web: http://www.hit.ac.il http://www.hit.ac.il/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Error during grompp
Furthemore the same part of the protein always move out of the box in different simulations. Is there any way to prevent the moving? http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
