On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos wrote:
Hi, I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor. When I try to use grompp it says atomtype opls_XXXX not found. I have added all the needed atoms in atomtypes.atp of the ff I want to use. I should also mention that I used an existing atom in atomtypes and then the ones I added. Also I used grep to see if I made any spelling mistakes.
The .atp file is used only by pdb2gmx. You need to add parameters in ffnonbonded.itp for any new atom types; this is what grompp is complaining about.
-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.
