RE: [gmx-users] methanol simulation error

- 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

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

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 g

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 CM

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.

[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.

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

[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