Dear Dr.Lemkul,
Thank you very much for your reply. It was very helpful to me. I checked the force field .rtp files. Here I have two questions: 1-Checking the .rtp files of gromos force field, I saw that always one hydrogen of NH2 and also the OH group of COOH were not included in the charge groups. On the other hand, in your paper ( Practice Consideration for building GROMOS-Compatiple Small-Molecule Topologies) I noticed that you have replaced these NH2 and COOH groups with NHCH3 and COCH3. I did not understand this. Would you please explain why you did that ? Should we do the same modifications for all NH2 and COOH groups, either when these groups belong to an aminoacid or any other molecule? 2- Is there any straightforward strategy for specifying charge groups of a ligand? If so, could you please introduce me a reference for that? As always, your response would be greatly appreciated. N.P On Sunday, June 8, 2014 11:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 6/8/14, 2:34 PM, Negar Parvizi wrote: > Dear Gromacs Users, > > Does anyone know, where can i find information about "Gromos96 building > blocks for suitable chargegroupings"? > Look in the force field .rtp files. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
