Re: [gmx-users] OPLS-AA forcefield
you zou wrote: Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. There is no difference. The presence of /L simply indicates it is for liquid simulations. I am unaware of a vacuum or gas phase OPLS-AA, certainly not within Gromacs. -Justin Thank you Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] OPLS-AA forcefield
Justin A. Lemkul skrev: you zou wrote: Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. There is no difference. The presence of /L simply indicates it is for liquid simulations. I am unaware of a vacuum or gas phase OPLS-AA, certainly not within Gromacs. -Justin I think that's incorrect. The 'L' in OPLS stands for 'Liquid'. The trailing /L was added when some parameters were reparameteriezd (dihedrals I think) at some point, but I don't know what it stands for. Erik Thank you Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS-AA forcefield
Erik Marklund wrote: Justin A. Lemkul skrev: you zou wrote: Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. There is no difference. The presence of /L simply indicates it is for liquid simulations. I am unaware of a vacuum or gas phase OPLS-AA, certainly not within Gromacs. -Justin I think that's incorrect. The 'L' in OPLS stands for 'Liquid'. The trailing /L was added when some parameters were reparameteriezd (dihedrals I think) at some point, but I don't know what it stands for. Oops, you're quite right! My mistake. I was thinking of the wrong L :) The /L indicates the use of local MP2 (LMP2) for parameterization. -Justin Erik Thank you Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] OPLS-AA forcefield parameters
Jacob Harvey wrote: Dear All, I am trying to use the OPLS-AA force field to model some imidazole containing compounds. I've noticed that imidazole units are referenced in the ffoplsaa.atp file as the following: opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in imidazole opls_559 14.00670 ; N3 in imidazole opls_560 12.01100 ; C4 in imidazole opls_561 12.01100 ; C5 in imidazole opls_5621.00800 ; H1 in imidazole opls_5631.00800 ; H2 in imidazole opls_5641.00800 ; H4 in imidazole opls_5651.00800 ; H5 in imidazole But there are no parameters for these atoms in the ffoplsaa.rtp file. Does anyone know how I can go about naming these atoms in my pdb file? Thank you in advance. Not every compound is present in a .rtp file. Check out its contents and you'll see what it has - pretty much just amino acids. The charges on each atom are not specific to an atom type, they are specific to a chemical species for which the parameterization scheme has been conducted. Lennard-Jones parameters are specified in ffoplsaanb.itp. I suggest a thorough read of Chapter 5 of the manual to understand the contents of these database-type files, and how they are used in assembling a topology. -Justin Jacob Harvey -- -- Jacob Harvey Graduate Student University of Massachusetts Amherst j.ha...@gmail.com mailto:j.ha...@gmail.com ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS-AA forcefield parameters
Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have residues in my system, because I am not modeling a protein. So I am not sure what to put in the residue name column. Gromacs does work on molecules that are not proteins correct? My molecules are histidine like so I tried putting HIS as the residue name, but I got the error: Fatal error: Residue 'H' not found in residue topology database When I dont put anything in that column I get the error: Fatal error: Residue '' not found in residue topology database And when I just generically call everything solvent and put SOL in that column I get: Fatal error: Residue 'S' not found in residue topology database You get the picture here. Does anyone have any solutions to my residue naming problem? Thank you. here is my pdb file: HETATM1 CT 2 -4.438 3.334 2.988 HETATM2 CT 2 0.588 3.313 0.517 HETATM3 CT 2 5.476 3.310 -2.216 HETATM4 HC 2 -4.134 2.590 3.731 HETATM5 HC 2 -5.525 3.438 3.047 HETATM6 HC 2 -3.996 4.291 3.276 HETATM7 HC 2 1.480 3.111 1.117 HETATM8 HC 2 -0.266 3.349 1.200 HETATM9 HC 2 0.702 4.307 0.076 HETATM 10 HC 2 6.375 3.525 -1.633 HETATM 11 HC 2 4.648 3.862 -1.761 HETATM 12 HC 2 5.628 3.709 -3.223 HETATM 13 CT 2 -3.996 2.922 1.581 HETATM 14 HC 2 -2.902 2.862 1.545 HETATM 15 HC 2 -4.281 3.703 0.865 HETATM 16 CT 2 0.394 2.242 -0.557 HETATM 17 HC 2 -0.485 2.486 -1.167 HETATM 18 HC 2 1.250 2.252 -1.242 HETATM 19 CT 2 5.188 1.805 -2.247 HETATM 20 HC 2 6.018 1.286 -2.742 HETATM 21 HC 2 4.300 1.615 -2.864 HETATM 22 CT 2 -4.587 1.582 1.127 HETATM 23 HC 2 -5.682 1.638 1.161 HETATM 24 HC 2 -4.298 0.792 1.828 HETATM 25 CT 2 0.235 0.836 0.028 HETATM 26 HC 2 -0.616 0.818 0.720 HETATM 27 HC 2 1.117 0.581 0.625 HETATM 28 CT 2 4.981 1.206 -0.852 HETATM 29 HC 2 4.152 1.720 -0.350 Jacob Harvey On Sat, Apr 4, 2009 at 2:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jacob Harvey wrote: Dear All, I am trying to use the OPLS-AA force field to model some imidazole containing compounds. I've noticed that imidazole units are referenced in the ffoplsaa.atp file as the following: opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in imidazole opls_559 14.00670 ; N3 in imidazole opls_560 12.01100 ; C4 in imidazole opls_561 12.01100 ; C5 in imidazole opls_5621.00800 ; H1 in imidazole opls_5631.00800 ; H2 in imidazole opls_5641.00800 ; H4 in imidazole opls_5651.00800 ; H5 in imidazole But there are no parameters for these atoms in the ffoplsaa.rtp file. Does anyone know how I can go about naming these atoms in my pdb file? Thank you in advance. Not every compound is present in a .rtp file. Check out its contents and you'll see what it has - pretty much just amino acids. The charges on each atom are not specific to an atom type, they are specific to a chemical species for which the parameterization scheme has been conducted. Lennard-Jones parameters are specified in ffoplsaanb.itp. I suggest a thorough read of Chapter 5 of the manual to understand the contents of these database-type files, and how they are used in assembling a topology. -Justin Jacob Harvey -- -- Jacob Harvey Graduate Student University of Massachusetts Amherst j.ha...@gmail.com mailto:j.ha...@gmail.com ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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
Re: [gmx-users] OPLS-AA forcefield parameters
Jacob Harvey wrote: Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have residues in my system, because I am not modeling a protein. So I am not sure what to put in the residue name column. Gromacs does work on molecules that are not proteins correct? My molecules are histidine like so I tried putting HIS as the residue name, but I got the error: If you want to use pdb2gmx to automatically generate your topology, you have to ensure that the appropriate .rtp entry is present within the desired force field and has the same name as the building block you are trying to use (again, this is spelled out in Chapter 5 of the manual). If you call your molecule HIS, then pdb2gmx will not magically build a random molecule; it will try to build histidine, based on the [ HIS ] entry in the .rtp file, so it will look for the exact atomic entries for histidine, no more no less. If you want a topology for an arbitrary molecule, you *can not* use pdb2gmx (unless you build the .rtp entry yourself). You will have to build it by hand, or use another program to build the .top file. I just uploaded a script I wrote to build an OPLS-AA topology from a .pdb file to the Users Contributions section on the website, but it does not assign atom types or charges (yet); it is up to you to assign the parameters and verify them. Fatal error: Residue 'H' not found in residue topology database Because it is not histidine. When I dont put anything in that column I get the error: Fatal error: Residue '' not found in residue topology database Because of a formatting error (the fact that your residue is either blank, or the number 2). And when I just generically call everything solvent and put SOL in that column I get: Fatal error: Residue 'S' not found in residue topology database Probably another formatting issue. But none of the above actually solve your problem, you're just trying to fool pdb2gmx into being magic, which it is not. -Justin You get the picture here. Does anyone have any solutions to my residue naming problem? Thank you. here is my pdb file: HETATM1 CT 2 -4.438 3.334 2.988 HETATM2 CT 2 0.588 3.313 0.517 HETATM3 CT 2 5.476 3.310 -2.216 HETATM4 HC 2 -4.134 2.590 3.731 HETATM5 HC 2 -5.525 3.438 3.047 HETATM6 HC 2 -3.996 4.291 3.276 HETATM7 HC 2 1.480 3.111 1.117 HETATM8 HC 2 -0.266 3.349 1.200 HETATM9 HC 2 0.702 4.307 0.076 HETATM 10 HC 2 6.375 3.525 -1.633 HETATM 11 HC 2 4.648 3.862 -1.761 HETATM 12 HC 2 5.628 3.709 -3.223 HETATM 13 CT 2 -3.996 2.922 1.581 HETATM 14 HC 2 -2.902 2.862 1.545 HETATM 15 HC 2 -4.281 3.703 0.865 HETATM 16 CT 2 0.394 2.242 -0.557 HETATM 17 HC 2 -0.485 2.486 -1.167 HETATM 18 HC 2 1.250 2.252 -1.242 HETATM 19 CT 2 5.188 1.805 -2.247 HETATM 20 HC 2 6.018 1.286 -2.742 HETATM 21 HC 2 4.300 1.615 -2.864 HETATM 22 CT 2 -4.587 1.582 1.127 HETATM 23 HC 2 -5.682 1.638 1.161 HETATM 24 HC 2 -4.298 0.792 1.828 HETATM 25 CT 2 0.235 0.836 0.028 HETATM 26 HC 2 -0.616 0.818 0.720 HETATM 27 HC 2 1.117 0.581 0.625 HETATM 28 CT 2 4.981 1.206 -0.852 HETATM 29 HC 2 4.152 1.720 -0.350 Jacob Harvey On Sat, Apr 4, 2009 at 2:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jacob Harvey wrote: Dear All, I am trying to use the OPLS-AA force field to model some imidazole containing compounds. I've noticed that imidazole units are referenced in the ffoplsaa.atp file as the following: opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in imidazole opls_559 14.00670 ; N3 in imidazole opls_560 12.01100 ; C4 in imidazole opls_561 12.01100 ; C5 in imidazole opls_5621.00800 ; H1 in imidazole opls_5631.00800 ; H2 in imidazole opls_5641.00800 ; H4 in imidazole opls_5651.00800 ; H5 in imidazole But there are no parameters for these atoms in the ffoplsaa.rtp file. Does anyone know how I can go about naming these atoms in my pdb file? Thank you in advance. Not every compound is present in a .rtp file. Check out its contents and you'll see what it has - pretty much just amino acids. The charges on
Re: [gmx-users] OPLS-AA forcefield parameters
Jacob Harvey wrote: Justin, How do I go about running topolgen on a linux system? There doesn't seem to be instructions for use, but I'm not familiar with perl scripts. Also I'd just like to say thank you for all your help. You've been really good with responding to my e-mail. I know that you have referenced chapter 5 in the manual multiple times, and I can assure you that I have read that chapter several times. I am a first year graduate student who is very new to molecular dynamics so some of the material is not trivial to me. Thank you again! To execute: perl topolgen.pl input.pdb Guess I forgot to include that in the README; my mistake. I'm working on making the script better, so I'll update that for a future release. Also be warned that I have not extensively tested the script beyond some basic small molecules. Please run some test simulations before collecting any real data. There are also a number of tutorials on the Gromacs wiki. The one written by Tsjerk is especially good at diagramming the flow of the programs, input/output, and how everything is put together. If you are unfamiliar with Gromacs, try out some tried-and-true methodology on known systems before simulating some bizarre system. It will save you a lot of headaches. -Justin Jacob Harvey On Sat, Apr 4, 2009 at 3:17 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jacob Harvey wrote: Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have residues in my system, because I am not modeling a protein. So I am not sure what to put in the residue name column. Gromacs does work on molecules that are not proteins correct? My molecules are histidine like so I tried putting HIS as the residue name, but I got the error: If you want to use pdb2gmx to automatically generate your topology, you have to ensure that the appropriate .rtp entry is present within the desired force field and has the same name as the building block you are trying to use (again, this is spelled out in Chapter 5 of the manual). If you call your molecule HIS, then pdb2gmx will not magically build a random molecule; it will try to build histidine, based on the [ HIS ] entry in the .rtp file, so it will look for the exact atomic entries for histidine, no more no less. If you want a topology for an arbitrary molecule, you *can not* use pdb2gmx (unless you build the .rtp entry yourself). You will have to build it by hand, or use another program to build the .top file. I just uploaded a script I wrote to build an OPLS-AA topology from a .pdb file to the Users Contributions section on the website, but it does not assign atom types or charges (yet); it is up to you to assign the parameters and verify them. Fatal error: Residue 'H' not found in residue topology database Because it is not histidine. When I dont put anything in that column I get the error: Fatal error: Residue '' not found in residue topology database Because of a formatting error (the fact that your residue is either blank, or the number 2). And when I just generically call everything solvent and put SOL in that column I get: Fatal error: Residue 'S' not found in residue topology database Probably another formatting issue. But none of the above actually solve your problem, you're just trying to fool pdb2gmx into being magic, which it is not. -Justin You get the picture here. Does anyone have any solutions to my residue naming problem? Thank you. here is my pdb file: HETATM1 CT 2 -4.438 3.334 2.988 HETATM2 CT 2 0.588 3.313 0.517 HETATM3 CT 2 5.476 3.310 -2.216 HETATM4 HC 2 -4.134 2.590 3.731 HETATM5 HC 2 -5.525 3.438 3.047 HETATM6 HC 2 -3.996 4.291 3.276 HETATM7 HC 2 1.480 3.111 1.117 HETATM8 HC 2 -0.266 3.349 1.200 HETATM9 HC 2 0.702 4.307 0.076 HETATM 10 HC 2 6.375 3.525 -1.633 HETATM 11 HC 2 4.648 3.862 -1.761 HETATM 12 HC 2 5.628 3.709 -3.223 HETATM 13 CT 2 -3.996 2.922 1.581 HETATM 14 HC 2 -2.902 2.862 1.545 HETATM 15 HC 2 -4.281 3.703 0.865 HETATM 16 CT 2 0.394 2.242 -0.557 HETATM 17 HC 2 -0.485 2.486 -1.167 HETATM 18 HC 2
