[gmx-users] Output of rotation
Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb file was visualized and its format seems to be correct. Anybody knows what is the problem? How can I overcome this problem? Please help me Thanks in advance. Sincerely, Shima -- 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] on tpbconv
Yes it will work .. Just at the time of mdrun add -cpi cpt ( prvious cpt file ) With best wishes and regards..!! On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, for my original MD, based on mdp file the total time is 500 ps. After it finished, I have decided to extend the MD run to 2.5 ns. I think the following command should be used: tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr But as for in the original mdp file the total time is 500 ps,is the -extend 2000 workable in the tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr? Do I need to change the total time in the original mdp file from 500 ps to 2000 ps or a time period longer than 2000 ps, after the original 500 pd finished, in order to make tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr workable? I am looking forward to getting your reply. Cheers, Acoot -- 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] Output of rotation
Hi Shima, How did you rotate the structure? Probably the TER records got lost in the process. Cheers, Tsjerk On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb file was visualized and its format seems to be correct. Anybody knows what is the problem? How can I overcome this problem? Please help me Thanks in advance. Sincerely, Shima -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Output of rotation
The input file has TER between 2 monomers. The command which I use is: #editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro After that, I use editconf to convert .gro to .pdb file: #editconf -f protein-rotate.gro -o protein.pdb The residue numbers after 10th one of output pdb file are changed and not correct. Sincerely, Shima - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, September 30, 2012 12:17 PM Subject: Re: [gmx-users] Output of rotation Hi Shima, How did you rotate the structure? Probably the TER records got lost in the process. Cheers, Tsjerk On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb file was visualized and its format seems to be correct. Anybody knows what is the problem? How can I overcome this problem? Please help me Thanks in advance. Sincerely, Shima -- gmx-users mailing list 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. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Calculate Density with respect to time...
Thank you for your immediate reply.. I need the xvg graph that will tell me the density of water in between the protein with respect to time . g_densmap not give such out put.. Sol please would you tell me how to do it ??? How to select the Sol that are only in between the protein ?? Thank you in advance.. With best wishes and regards Rama David -- 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] .itp and .rtp file modifications?
On 9/29/12 11:47 PM, Elie M wrote: Dear all, I am trying to minimize the energy of a polymer system I have. I have successfully modified the n2t file to include force fields for atoms that were not present. However now I am using grompp before using mdrun (to minimize). However I have a question should the .ITP and .RTP files be modified accordingly and if yes how is this possible? Any information of how to modify them? If g_x2top is providing you with a suitable topology, then no adjustments need to be made. g_x2top uses .n2t files like pdb2gmx uses .rtp files - they provide the building blocks for topologies. -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] number of coordinates in coordinate file does not match topology -reg
On 9/30/12 1:06 PM, venkatesh s wrote: Respected gromacs users now iam buliding the simulation system for protein + peptide simulation (manually insert the peptide into the protein structure file after the TER ) following commands i used here 1. pdb2gmx -f 2KW8.pdb -o lpvtg.gro -water tip3p -ignh -chainsep ter in topol.top file i manually made change as a Protein_chain_A 2 (previously it is 1) [ molecules ] ; Compound#mols Protein_chain_A 2 This does not sound correct to me. You have a large protein and a small peptide, correct? These should be different proteins and different [moleculetype] entries, correct? If this is true, you have two distinct proteins, not two copies of the same one. 2. editconf -f lpvtg.gro -o lpvtg_newbox.gro -c -d 1.0 -bt dodecahedron 3. genbox -cp lpvtg_newbox.gro -cs spc216.gro -o lpvtg_solv.gro -p topol.top 4. grompp -f ions.mdp -c lpvtg_solv.gro -p topol.top -o lpvtg_ions.tpr fatal error number of coordinates in coordinate file (lpvtg_solv.gro, 24393) does not match topology (topol.top, 26811) and i read following link http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology manually may want update topol.top file, if yes can you explain? I think you need to revisit step 1. -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] Re: g_wham
Please keep all Gromacs-related correspondence on the gmx-users mailing list. I am CC'ing this message there and would ask that all further correspondence be posted to the list so that you can benefit from commentary from the entire community. See comments below. On 9/30/12 2:09 PM, Chris Shuck wrote: Hello, I'm hoping you can help me with this. I was running umbrella sampling and was having an issue. In running g_wham I get this error: Program g_wham, VERSION 4.5.5 Source code file: futil.c, line: 459 File input/output error: histo.xvg For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I used the following command: g_wham -it umb.dat -if pullf.dat -o -hist -unit kCal umb.dat contains: umbrella0.tpr umbrella1.tpr ... etc pullf.dat contains: pullf-umbrella0.xvg pullf-umbrella1.xvg ...etc Now, the issue I may be experiencing could be due to what I have in the folder. I do not have the TRR files in this folder, only GRO, XTC, and XVG files. Is that an issue? I was under the impression that g_wham does not require TRR or LOG files. Can you shed any light on this issue? I/O errors suggest you do not have sufficient read/write permissions on the working directory or perhaps enough disk space. You do not need anything beyond .tpr and and .xvg files in the working directory. From your description, it seems you do not have the .tpr files there, so that could be one potential problem, but I would expect a different error message in that case. -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] Error with grompp
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. Thanks in advance, Elie -- 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] DNA orientation restraint
Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX Manual. But the orientation value is set to be observables of NMR experiments, such as this example: ; ai aj type exp. label alpha 31 32 1 1 3 3 -- 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] DNA orientation restrain
Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX Manual. But the orientation value is set to be observables of NMR experiments, such as this example: ; ai aj type exp. label alpha const. obs. weight 31 32 1 1 3 3 6.083 -6.73 1.0 But how can I set the observable in my case as it's not an NMR experiment? Any suggestion will be appreciate. Thanks very much Dudu Tong 31%2032%201%201%203%203 -- 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
