[gmx-users] question about new residue

Justin Lemkul jalemkul at vt.edu
Mon Oct 1 23:01:46 CEST 2012

On 10/1/12 4:59 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
>   I want to do a md run. But I have a problem. I have additional residues
> which are not in the aminoacid.rtp file.
> I already read the site about "Adding a Residue to a Force Field".
> But the problem is that I am not allowed to change anything at the
> topology files on the server I want to run the job. I have to run it on
> this server because on my computer it would take way to long.
> So is there another possibility to add the new residues to the topology or
> offer them to gromacs.
> Or can I do all the preparing steps until the md run local on my computer
> where I already changed the topologies so that all the input files which
> aare produced by grompp and are needed by the md-run are already there.

You can do all the preparation steps on your own machine.  Alternatively, you 
can always make a copy of the force field directory (and its entire contents) in 
the working directory and make any changes there.  pdb2gmx will detect the 
directory in the working directory and use its files to generate the topology. 
Doing so circumvents any permission issues.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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