[gmx-users] PTFE polymer chain

Justin Lemkul jalemkul at vt.edu
Tue Apr 9 19:02:53 CEST 2013

Please keep the discussion on the gmx-users list.

On Tue, Apr 9, 2013 at 12:55 PM, luanadelorenzo at libero.it <
luanadelorenzo at libero.it> wrote:

> Hi Justin,
> thansk for the fast reply.
> The exact command is this:
> pdb2gmx -ff /home/user01/work/oplsaa.ff/ -f PTFE10.pdb -chainsep ter
> I have created this directory coping the oplssa.ff directory in share
> utilities (I'm  an user not an administrator of the pc) and I cannot modify
> the original files.
> I attach the files .pdb, and the files oplssa.rtp ffgmx.rtp and
> residuetypes.dat that I have modified addying the new residues. (I have
> also modifed specbond.dat for the two bonds between internal residue and
> starting/terminal residues.
> I don know if I made mistakes or simply I use bad the command.
The command is incorrect. The -ff flag takes only the prefix of the force
field you're trying to use. Your command is going to look for a directory
called /home/user01/work/oplsaa.ff/.ff, which of course does not exist. Put
the custom oplsaa.ff directory in your working directory and issue pdb2gmx
without the -ff flag. pdb2gmx will prompt you to choose the force field,
allowing you to differentiate between oplsaa.ff in the working directory
vs. the one in $GMXLIB.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


More information about the gromacs.org_gmx-users mailing list