[gmx-users] PTFE polymer chain

Justin Lemkul jalemkul at vt.edu
Tue Apr 9 18:24:35 CEST 2013

On Tue, Apr 9, 2013 at 12:21 PM, luanadelorenzo at libero.it <
luanadelorenzo at libero.it> wrote:

> Hi
> I'm a new user of Gromacs and I want to construct a linear chain of
> polytetrafluoroethylene using the force field oplsaa.
> I created  a work directory and I modified the rtp files by introducing 3
> new residues corresponding to my starter of chain (TFEa), my internal
> residue (TFEi), and my terminal residue (TFEb)(following the same procedure
> descirbed by Justin for Polyethylene) I add these new three residue to the
> residuetypes.dat as Other.
> When I run pdb2gmx with the -ff option (for using my modified force field)
> the message of error is the following:
> Could not find force field '/home/user01/work/oplsaa.ff/' in current
> directory, install tree or GMXDATA path.
> If I use pdb2gmx without using the command -ff the error is always the
> same:
> Fatal error:
> Residue 'TFEa' not found in residue topology database
> How can I solve this problem? Could someone help me?

It would be helpful to see your exact command, because my suspicion is
you're invoking pdb2gmx incorrectly (it looks like you're specifying a
path, rather than just a base force field name). The modified .ff directory
needs to be either in $GMXLIB or in the working directory. If you omit -ff
altogether, pdb2gmx will detect it automatically and allow you to
interactively choose it.




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


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