[gmx-users] Constraint of active site in gromacs

[Raj D]

Thanks Justin, Is there any tool to convert itp file contents to gromacs
formated ff file ?
 On May 7, 2015 5:23 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 5/7/15 6:33 AM, Raj D wrote:
>
>> Dear Mark,
>>
>> So to make distance restrain of specific  atoms of  protein residues and
>> the ligand (itp  file produced by antechamber), I may have to cut the
>> ligating atoms of amino acids in the  topology as produced by pdb2gmx and
>> paste into the ligand.itp to make the distance restraint to work ...Is it
>> the right approach to bring all distance restrained atoms to bring into
>> the
>> same molecule type ?
>>
>
> You can't have a separate ligand topology for this to work.  It literally
> needs to be a merged [moleculetype] for everything that will participate in
> distance restraints.  That requires creation of an .rtp entry (not .itp
> file) for pdb2gmx to use in creating the topology, in concert with the
> -merge option.
>
> -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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