[gmx-users] Query- Ligand topology

[Priya Das]

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?*

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