R: Re: Re: [gmx-users] PTFE polymer chain

[luanadelorenzo at libero.it]

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't  know if I made mistakes or simply I use badly the command.
Thanks for the fast reply.Luana.






----Messaggio originale----

Da: jalemkul at vt.edu

Data: 09/04/2013 19.02

A: "luanadelorenzo at libero.it"<luanadelorenzo at libero.it>, "Discussion list for GROMACS users"<gmx-users at gromacs.org>

Ogg: Re: Re: [gmx-users] PTFE polymer chain




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
-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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