RE: [gmx-users] methanol simulation error
Please copy and paste in here the contents of your .top file. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mustafa bilsel Sent: Friday, 7 January 2011 12:32 PM To: gmx-users@gromacs.org Subject: [gmx-users] methanol simulation error Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- 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] methanol simulation error
On 7/01/2011 12:31 PM, mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. I'm not sure why I'm repeating myself, but the name given in that moleculetype is not SOL. That name must match what appears in the [molecules] section. Please make sure you have read the examples in Chapter 5 of the manual and understand everything there. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? You're using atomtype CMET somewhere in your .top or its #included .itp files. Your forcefield doesn't define atomtype CMET, and it needs to if your usage is correct. Without seeing your topology, we can't say more. 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] methanol simulation error
mustafa bilsel wrote: Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I will assume you're not using the current version of Gromacs. This was a bug that was fixed some time ago. Please upgrade to version 4.5.3. I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Is SOL the appropriate name given in the [moleculetype] directive for methanol? The name "SOL" is the default name for water in Gromacs, so this may be where you're having problems. Just because methanol is a solvent doesn't mean it should be named SOL. Check the name in the topology to be sure this is what you should be using. -Justin Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- 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/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] methanol simulation error
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[gmx-users] methanol simulation error
Hi all, I try to make a simulation in methanol. I use gromos43a1 forcefield. My command follow, pdb2gmx -f xxx.pdb editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro When grompp for minimization it gives an error: Atomtype CMET not found I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. Also I added #include "gromos43a1.ff/methanol.itp" line to .top. Please don't suggest non-water solvation in how-to part of Gromacs web. Could you tell me what missing is? best wishes mustafa -- 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] methanol simulation
mustafa bilsel wrote: Dear Mark, so, what should I do? In the future, it would be helpful to reply to the original thread instead of starting a new one. You said you added a line "SOL 291" to your [molecules] directive. That would imply that you named your methanol [moleculetype] SOL. If this is not the case, then you're providing an invalid name, and hence the fatal error. -Justin mustafa -- 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/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] methanol simulation
Dear Mark, so, what should I do? mustafa -- 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] methanol simulation
On 6/01/2011 10:35 PM, mustafa bilsel wrote: Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I have used pdb2gmx -f xxx.pdb , that is, I haven't added anything like in water simulation -water tip3p. Should we add something to tell the gromacs that it is methanol simulation? The [ molecules ] section of your .top lists the names you gave to the [ moleculetypes ] and the number of such molecules. Apparently you gave no moleculetype the name "SOL"... 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] methanol simulation
Hi all, I have the following error in grompp before energy minimization: No such moleculetype SOL I have used grep to count the methanol molecules and added SOL 291 comment in .top file to tell the number of methanols. What is missing there? Note: I have used pdb2gmx -f xxx.pdb , that is, I haven't added anything like in water simulation -water tip3p. Should we add something to tell the gromacs that it is methanol simulation? best wishes mustafa -- 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
