On 4/7/15 7:53 AM, Sneha Menon wrote:
Dear all, I want to simulate a polymer - triphenylphosphine connected to a polyethylene glycol polymer using the CHARMM36 forcefield. I obtained the parameters of this polymer (resname TPP) using SwissParam. I added this molecule to the forcefield by following all the steps mentioned in : http://www.gromacs.org/Documentation/Hotos/Adding_a_Residue_to_a_Force_Field I want to embed this polymer into a lipid bilayer. I first tried to make a topology file for the polymer using : *pdb2gmx -f file.pdb -o file.gro* However, it showed up the following error: Fatal error: Residue 1 named TPP of a molecule in the input file was mapped to an entry in the topology database, but the atom 16 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I compared the .rtp file as well as the input .pdb file for any missing atoms. I could not find any atoms missing or discrepancy in the atom/residue naming. What else could be the problem?
You need to provide the relevant snippets of the .rtp and .pdb files. Something is missing or mismatched, otherwise pdb2gmx would not complain.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
