[gmx-users] (no subject)
Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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] (no subject)
Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well. Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property. By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder). It would be good if you explain what you are trying to do in detail to get more productive help. Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Monday, 25 March 2013 5:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] (no subject) Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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] problem in converting coarse grained structure to fine strcture
Dear gromacs users, I used the command g_fg2cg to convert a coarse grained structure into corresponding fine strcture, and i found that the water molecues can be transformed correctly, but there is a big mess in the protien , and i could not get correct protein strcture, can anyone give me some suggestion? BW Fugui -- 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] (no subject)
On 3/25/13 2:37 AM, Emanuel Birru wrote: Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well. The directive is [dihedraltypes]. One can differentiate between propers and impropers by looking at the function type (see Table 5.5 in the manual). Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property. Atom names are not what ffbonded.itp uses. Interaction types are defined by atom types. -Justin By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder). It would be good if you explain what you are trying to do in detail to get more productive help. Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Monday, 25 March 2013 5:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] (no subject) Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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] (no subject)
Thanks Justin, sorry for using the wrong word what I had to mention was atom type not name. Jeremy, as per Justin's comment I guess you better work out what kind of parameters you have to use for your impropers. The functions that you should put in you ligand itp file should be the same as amber ff. Cheers, On 25/03/2013, at 9:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/25/13 2:37 AM, Emanuel Birru wrote: Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well. The directive is [dihedraltypes]. One can differentiate between propers and impropers by looking at the function type (see Table 5.5 in the manual). Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property. Atom names are not what ffbonded.itp uses. Interaction types are defined by atom types. -Justin By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder). It would be good if you explain what you are trying to do in detail to get more productive help. Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Monday, 25 March 2013 5:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] (no subject) Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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] Re: Re: help with chromophore of a GFP
Dear gmx-users, I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. I'm trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated by Antechamber. To date, I've added those parameters related to bonds, now I have to add those related to angles, dihedrals and impropers. I'm dealing with section [angletypes] of file ffbonded.itp, and I'm looking at the values of cth (that I imagine is the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see that all parameters in ffbonded.itp are multiple of the value of 4.184, corresponding to the conversion factor between kcal and kJ. If I divide each of these values, I obtain a value corresponding to a number such as 80, 70, 120, 40 etc. Instead, if I look at those corresponding values found using Antechamber, I see, as expected, numbers with decimals, that are often very different from those present in ffbonded.itp (when I compare angles present in both files). For example, for the angle CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72 kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of 63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which is different from the value of Antechamber. If I consider the angle CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is 46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184 is exactly 100. Moreover, the same values of angles and forces are applied to angles that in my opinion are quite different among them. For example, I found the same value of 109.5 (th) and 418.4 (cth) for: H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1, H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very different to me, and I'd expect to find different values of these parameters. It seems to me that values into ffbonded.itp related to these force constants are quite strange, especially for the fact that they are EXACTLY multiple of 4.184, and I wonder if I'm correctly interpreting these values. Best regards Anna -- 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] position restraints
Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define = -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. 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] position restraints
On 3/25/13 12:06 PM, Shima Arasteh wrote: Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define= -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Again, POSRE and POSRES are different. -DPOSRES will not trigger the #ifdef POSRE block. -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] position restraints
Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. define = -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? Thanks for help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 8:52 PM Subject: Re: [gmx-users] position restraints On 3/25/13 12:06 PM, Shima Arasteh wrote: Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define = -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Again, POSRE and POSRES are different. -DPOSRES will not trigger the #ifdef POSRE block. -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] position restraints
On 3/25/13 1:40 PM, Shima Arasteh wrote: Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. I believe what I see. If you're trying to re-type from memory what's in your topology and/or .mdp file, that's not productive. Please copy and paste to make efficient use of everyone's time. define= -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? I've been trying, and it appears you're either giving inconsistent or incorrect information. Copy and paste directly from your .top file whatever sections are relevant. You also haven't said what is in lipid_posre.itp, which can be another source of problems. You just said you've created it with genrestr, but you didn't say what group you included. The numbering in the position restraint file is per [moleculetype], not the global atom numbering in the coordinate file. -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] position restraints
Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 10:13 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:40 PM, Shima Arasteh wrote: Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. I believe what I see. If you're trying to re-type from memory what's in your topology and/or .mdp file, that's not productive. Please copy and paste to make efficient use of everyone's time. define = -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? I've been trying, and it appears you're either giving inconsistent or incorrect information. Copy and paste directly from your .top file whatever sections are relevant. You also haven't said what is in lipid_posre.itp, which can be another source of problems. You just said you've created it with genrestr, but you didn't say what group you included. The numbering in the position restraint file is per [moleculetype], not the global atom numbering in the coordinate file. -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 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 -- 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] position restraints
On 3/25/13 1:50 PM, Shima Arasteh wrote: Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.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 ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 POPC238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. In that case, lipid_posre.itp should have only one line. If you've made an index group of multiple P atoms across multiple molecules, that is the incorrect approach. Consult the manual, website, and numerous threads in the archive. -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] position restraints
Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 10:22 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:50 PM, Shima Arasteh wrote: Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. In that case, lipid_posre.itp should have only one line. If you've made an index group of multiple P atoms across multiple molecules, that is the incorrect approach. Consult the manual, website, and numerous threads in the archive. -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] position restraints
On 3/25/13 2:47 PM, Shima Arasteh wrote: Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? What you need to understand is how the position restraint mechanism works. If you know that, you can make .itp files by hand using a text editor if you like (which is actually what I do in the case of one-liners like lipid_posre.itp for what you're doing). -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] position restraints
Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. Thanks Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 11:20 PM Subject: Re: [gmx-users] position restraints On 3/25/13 2:47 PM, Shima Arasteh wrote: Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? What you need to understand is how the position restraint mechanism works. If you know that, you can make .itp files by hand using a text editor if you like (which is actually what I do in the case of one-liners like lipid_posre.itp for what you're doing). -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 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 -- 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] position restraints
On 3/25/13 3:00 PM, Shima Arasteh wrote: Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. I would again suggest focusing more on the position restraints contents themselves. Your formulation for #including them is correct. The contents of lipid_posre.itp are not. There is substantial discussion on the topic of position restraints in the manual, as well as the help description of genrestr (especially the part that starts with WARNING), which I am willing to bet will solve your issues if you read it carefully. -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] Re: Re: help with chromophore of a GFP
On Mon, Mar 25, 2013 at 4:56 PM, Anna MARABOTTI amarabo...@unisa.it wrote: Dear gmx-users, I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. I'm trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated by Antechamber. To date, I've added those parameters related to bonds, now I have to add those related to angles, dihedrals and impropers. I'm dealing with section [angletypes] of file ffbonded.itp, and I'm looking at the values of cth (that I imagine is the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see Yes, table 5.5 is definitive. that all parameters in ffbonded.itp are multiple of the value of 4.184, corresponding to the conversion factor between kcal and kJ. If I divide each of these values, I obtain a value corresponding to a number such as 80, 70, 120, 40 etc. These are (should be) based on the original definition in the AMBER force field. Instead, if I look at those corresponding values found using Antechamber, I see, as expected, numbers with decimals, that are often very different from those present in ffbonded.itp (when I compare angles present in both files). For example, for the angle CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72 kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of 63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which is different from the value of Antechamber. If I consider the angle CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is 46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184 is exactly 100. I gather you asked Antechamber to do an unconstrained optimization, so it did. That's clearly not so reasonable for incorporating the result into a force field that uses the same atom types. Either you need to use a different atom type for the newly-parameterized CT (perhaps by naming the atoms differently in the input to Antechamber) so there's no mismatch, or you need to explore how to constrain Antechamber's optimization (e.g. its documentation or the AMBER mailing list). Moreover, the same values of angles and forces are applied to angles that in my opinion are quite different among them. For example, I found the same value of 109.5 (th) and 418.4 (cth) for: H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1, H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very different to me, and I'd expect to find different values of these parameters. Welcome to the joys of parametrisation. If you were to parameterise each of those separately, you would need data that would be sensitive to each, and ideally more than one kind of data. The number of possible interaction types, the amount of parametrisation data required, and length of the overall optimisation process explodes fast (each parameter should be optimised in the context of *all* the others, remember). The additional value delivered by the specialised parameters would be low. So catch-all parameters are, unfortunately, common. It is not possible to model these interactions accurately with a single force constant that is valid in all chemical contexts of interest, so one has to give up at some point. It seems to me that values into ffbonded.itp related to these force constants are quite strange, especially for the fact that they are EXACTLY multiple of 4.184, and I wonder if I'm correctly interpreting these values. It sounds like the original parametrisation used a granularity of 10 kcal/mol for these force constants. Optimising any of the parameters to arbitrary precision is likely to lead to over-fitting the parameters to the data used for parametrisation. Losing the capacity to generalise to observables outside the parametrisation set is another hidden trap in the process. Fortunately, discretising the problem domain also speeds up the optimisation. 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] position restraints
Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 11:34 PM Subject: Re: [gmx-users] position restraints On 3/25/13 3:00 PM, Shima Arasteh wrote: Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. I would again suggest focusing more on the position restraints contents themselves. Your formulation for #including them is correct. The contents of lipid_posre.itp are not. There is substantial discussion on the topic of position restraints in the manual, as well as the help description of genrestr (especially the part that starts with WARNING), which I am willing to bet will solve your issues if you read it carefully. -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] position restraints
On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 001000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -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] position restraints
Ohhh...! :-) I could not get it on my own independently! Thanks for all your explanation! Many many thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 12:02 AM Subject: Re: [gmx-users] position restraints On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 0 0 1000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -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 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 -- 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: problem in converting coarse grained structure to fine strcture
Most probably you may not have described the [mapping] section for the protein in the topology file correctly. Check your topology file. From your description it is difficult to guess what is the exact problem. cheers - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.n6.nabble.com/problem-in-converting-coarse-grained-structure-to-fine-strcture-tp5006598p5006615.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Aw: [gmx-users] Re: Re: help with chromophore of a GFP
If you back the origional papers alot of the conversions can be found. I dont know the papers off the top of my head, so you should just ask your PI, collegues or the board. They are a pain, one paper will have 2 and be missing one definition you want, etc... Stephan Watkins Gesendet:Montag, 25. Mrz 2013 um 16:56 Uhr Von:Anna MARABOTTI amarabo...@unisa.it An:gmx-users@gromacs.org Betreff:[gmx-users] Re: Re: help with chromophore of a GFP Dear gmx-users, Im still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. Im trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated by Antechamber. To date, Ive added those parameters related to bonds, now I have to add those related to angles, dihedrals and impropers. Im dealing with section [angletypes] of file ffbonded.itp, and Im looking at the values of cth (that I imagine is the angle force constant expressed in kJ mol^-1 rad^-2, correct?) I see that all parameters in ffbonded.itp are multiple of the value of 4.184, corresponding to the conversion factor between kcal and kJ. If I divide each of these values, I obtain a value corresponding to a number such as 80, 70, 120, 40 etc. Instead, if I look at those corresponding values found using Antechamber, I see, as expected, numbers with decimals, that are often very different from those present in ffbonded.itp (when I compare angles present in both files). For example, for the angle CT-CT-CT (3 C sp3), I see in ffbonded.itp a value of cth equal to 334.72 kJ mol^-1 rad^-2. For the same angle, Antechamber calculated a value of 63.21 kcal/mol^-1 rad^-2. If I do 334.72/4.184 the result is 80, which is different from the value of Antechamber. If I consider the angle CT-CT-HC (2 C sp3 and one H) the angle force constant in Antechamber is 46.37 kcal mol-1 rad-2, in ffbonded.itp is 418.4, that divided by 4.184 is exactly 100. Moreover, the same values of angles and forces are applied to angles that in my opinion are quite different among them. For example, I found the same value of 109.5 (th) and 418.4 (cth) for: H2-CT-N*, H1-CT-N*, H1-CT-OH, H1-CT-OS, H2-CT-OS, N*-CT-OS, C-CT-H1, H1-CT-N2, C-CT-HC... All these angles involve atoms that seem very different to me, and Id expect to find different values of these parameters. It seems to me that values into ffbonded.itp related to these force constants are quite strange, especially for the fact that they are EXACTLY multiple of 4.184, and I wonder if Im correctly interpreting these values. Best regards Anna -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] Dihedral restraints
Hello All, While doing NMR refinement or custom force addition, it can happen than the force on the system can push the peptide plane atoms out of the plane. [ like the amide bond is pushed out of the plane to satisfy the external force or the omega angle is deformed beyond acceptable values]. To control this behavior, I want to employ dihedral restrains on my system. I have understood the format and the required steps but the results of a short simulation are not as expected. For example : #18 : C of resid 1 ; 20 : N of resid 2 ; 5 : CA of resid 1 ; 22 : CA of resid 2 # 19 : O of resid 1 ; 21 : H of resid 2. #; ai ajakal type label phi dphi kfac power 5 18 20 22 1 0 180.00 4 1 1 19 18 20 22 1 0 0.004 1 1 5 18 20 21 1 0 180.00 4 1 1 19 18 20 21 1 0 0.004 1 1 In the .mdp file, i have ;dihedral restraints dihre = yes dihre_fc= 50 ; or whatever value you desire nstdihreout = 50 I ran a short 2000 step simulation and over the period of time I tracked the four dihedral values, every row is a timestep. #the first line is the restrained reference value. 180 0 180 0 -147.287215895064 9.45865329024718-159.203988508429 -2.45811932311724 -111.050389450397 -81.9953887566147 -92.0822326476887 -63.0272319539059 -110.958596230868 -73.8376501933164 -92.9130172813275 -55.7920712437757 -112.517830994369 -59.5426717504823 -102.604122568900 -49.6289633250131 -100.996135584400 -74.4228693635875 -87.2297061267471 -60.6564399059348 -93.9669086707340 -57.7658765173159 -86.3382092652599 -50.1371771118417 -95.0591618723864 -66.9832558152160 -85.0934054990846 -57.0174994419143 -94.2190629339560 -52.6947808390542 -91.1562898592925 -49.6320077643907 -87.5354914279667 -69.2330638322494 -73.2840411103266 -54.9816135146093 -112.405078265351 -73.0596345313864 -97.4992184521689 -58.1537747182041 As you can see, the value moves away from the reference value as the simulation goes on. Any hints about any possible mistake in my implementation would be appreciated. Thanks Santhosh -- View this message in context: http://gromacs.5086.n6.nabble.com/Dihedral-restraints-tp5006617.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] scaling factor for rna/dna
dear gromacs users, I am doing LIE calculation in gromacs for RNA molecules, What scaling factor (alpha and beta) should i use for calculation? Is that default values for protein ligand will work'? how we can get these alpha and beta scaling factors for nucleic acid? thanks in advance.. Thanks and Regards, -- Vishwambhar Centre for Bioinformatics Pondicherry University Pondicherry -- Note: Strictly confidential to Vishwayogi -- 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] G54a7 compatibility with G53a6?
Hi All I have a membrane protein with a lot of alpha helices in it. I want to use the 54a7 parameters for the protein and Kukol parameters (modified 53a6) for the POPC membrane. Is this feasible? I know that there are issues with combining widely different ffs, but these forcefields seem very similar. Thanks, -- View this message in context: http://gromacs.5086.n6.nabble.com/G54a7-compatibility-with-G53a6-tp5006619.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
