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? Thanks! On Mon, Jul 27, 2015 at 5:43 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/23/15 2:10 AM, Ganesh Shahane wrote: > >> Dear Gromacs Users, >> >> I am looking forward to performing some simulations of a receptor bound to >> serotonin (also known as 5-HT). Does anybody have the .itp file of >> serotonin for the charmm27 or charmm36 force field? Thank you! >> >> > It's very straightforward to combine existing parameters to make this > simple molecule (indole + hydroxyl + alkyl amine). CHARMM covers all of > these functional groups easily. > > -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. > -- Best Regards, Ganesh Shahane -- 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.