RE: [gmx-users] methanol simulation error

2011-01-06 Thread Dallas Warren
- 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

2011-01-06 Thread Mark Abraham
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

2011-01-06 Thread Justin A. Lemkul
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

2011-01-06 Thread wibke . sudholt
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[gmx-users] methanol simulation error

2011-01-06 Thread mustafa bilsel
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