[gmx-users] Query- Ligand topology

[Mark Abraham]

On Sun, Mar 15, 2015 at 8:58 PM, Priya Das <priyadas001 at gmail.com> wrote:

> Thankyou for the reply .
> I tried to generate topology using Swiss Param website.
> <http://www.swissparam.ch/>
> Its somewhat trustworthy it seems.
>
> The only difference is that each 45 atoms of the ligand has unique charge
> group number.
> The assigning of charges are justified.
>
> *I have still a small query : Has the atom name in .itp file and .gro file
> has to be same?*
>

Strictly, no, grompp relies on order. But it will warn you if they are not
named the same, and it's your problem to make sure that they match
logically.

Mark

On Sun, Mar 15, 2015 at 5:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/15/15 6:50 AM, Priya Das wrote:
> >
> >> Dear all,
> >>
> >> I am submitting a ligand with 45 HETATM PDB file in PRODRG, but i get a
> >> result with 46 HETATM.
> >> The main error is in the -NH group, the structure generated by PRODRG
> >> shows
> >> four valence for Nitrogen.
> >>
> >
> > Changing protonation states is covered in the PRODRG FAQ.
> >
> >  Is there any other tool/option for generating the topology?
> >>
> >>
> > For GROMOS, try ATB.  At the very least, you need to be carefully
> > scrutinizing and re-optimizing the PRODRG charges and charge groups.  The
> > output is generally not very accurate.  Never trust a black box with
> > something so crucial :)
> >
> > -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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>
>
> --
> *Let us all join hands to save our " Mother Earth"*
> ------------------------------------------------------------------------
> Regards,
> Priya Das
> Research Scholar
> Dept. of Computational Biology and Bioinformatics,
> University of Kerala
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