[gmx-users] (no subject)

[Emran Heshmati]

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.agarwal800 at gmail.com>
 To: gmx-users at 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" <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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