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