On 7/27/15 1:03 AM, Ganesh Shahane wrote:
Hi Justin, Yes. I tried the same, but during the preparation of the .tpr file using grompp it gives an error saying "No default proper dihedral types" for 3 dihedral angles which are not present in the ffbonded.itp of the charmm36 force-field. These 3 dihedrals consist of atoms that encompass the alkyl amine and the indole groups of serotonin. Now, if I remove these dihedrals in question from the serotonin's .itp file which I have prepared, the simulation runs just fine. I am trying to calculate the free energy of solvation for serotonin. Considering this, is it okay to ignore some of these dihedrals?
Absolutely not. You can't just delete inconvenient interactions. If there are missing parameters, you need to derive suitable dihedral terms. Or just throw the molecule at ParamChem and see how it does. CGenFF should work fine for this molecule.
-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.
