On 11/3/17 4:49 AM, Adriano Santana Sanchez wrote:
Dear all, I am a beginner with gromacs and I have already done some online tutorials. I am now trying to create from a PDB coordinate file (a CTAB molecule) the corresponding .GRO and .TOP files to run MD simulations. gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce then choose FF gromos96 53a6 but get error message: Residue 'XXX' not found in topology database I am sure this FF has been used for this molecule before and I cannot find this CTAB on the residue database. What can I do?
pdb2gmx cannot process something it doesn't know about, so if a residue is not in the .rtp file, you can't use that force field unless you (1) find parameters in the literature and add them to the .rtp and force field files or (2) parametrize it yourself and subsequently add it.
-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.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
