On 10/4/18 11:28 AM, Raji wrote:
Thank you for your reply. I am trying to simulate this peptide in gromacs with CHARMM36 force field. Thatswhy i converted the parameters from CGenFF to CHARMM format. So How to proceed further. I assume i cant treat it like
The first step is to not use CGenFF to parametrize the custom residue.
as a protein ligand complex, because there is covalent bond between TYR and
It's just a protein, there is no ligand.
alkyl chain? And What is core CHARMM atom types?
By "core CHARMM atom types," I mean those that are already part of the C36 force field, not coming from CGenFF. If the second character of the atom type is "G" then you are using a CGenFF type. Don't.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
