[gmx-users] (no subject)

[Mark Abraham]

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.agarwal800 at 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" <jalemkul at 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
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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