[gmx-users] question about new residue

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Mon Oct 1 23:06:30 CEST 2012

Hi Justin,
 thank you very much for the helpful and fast answer :)

> 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
> --
> ========================================
> 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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