Hi, That's preliminary information you need to know about your ligand from its basic chemistry.
Mark On Fri, 16 Jun 2017 16:54 Shivangi Agarwal <shivangi.agarwal...@gmail.com> wrote: > Ya sir > But for ATB, it is asking for total charge. How to calculate total charge? > On 16 Jun 2017 18:59, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > > > > On 6/16/17 8:03 AM, Shivangi Agarwal wrote: > > > >> Hi all > >> > >> When i am generating a ligand topology using PRODRG, I am getting > topology > >> file with hydrogens deleted in it. Which another server can I use for > >> ligand topology generation? > >> > >> > > GROMOS is a united-atom force field, so the aliphatic H atoms are not > > going to be explicitly represented; you should check your assumptions > about > > force fields and which one you should be using if this comes as a > surprise > > :) PRODRG is not of sufficient quality for MD simulations without > > significant manual revision. ATB is better if you want to use a GROMOS > > parameter set. > > > > -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. > > > -- > 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. > -- 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.