total charge of your molecule depends on ionizable groups on your molecule and the pH. Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to
From: Shivangi Agarwal <shivangi.agarwal...@gmail.com> To: gmx-us...@gromacs.org Sent: Friday, 16 June 2017, 18:24 Subject: Re: [gmx-users] (no subject) 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.