On 10/1/12 4:59 PM, [email protected] 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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
