OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)?
Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Sunday, July 8, 2012 9:02 PM Subject: Re: [gmx-users] define a new residue On 7/8/12 11:29 AM, Shima Arasteh wrote: > Thanks all. > So if I find a protein which is parametrized by CHARMM and then find the > valine residue there, I might use the parameters of side chains of it in my > own rtp file. Right? > > You can look this up in the force field's .rtp file. For full parameterization procedures, refer to the primary literature for CHARMM. It should detail how to derive parameters for new species. -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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
