[gmx-users] Constraint of active site in gromacs

[Justin Lemkul]

On 5/7/15 8:13 AM, Raj D wrote:
> Thanks Justin, Is there any tool to convert itp file contents to gromacs
> formated ff file ?

Not that I'm aware of, but it's a simple exercise.  You have the hard part 
(parametrization) done.  Now you just need to write the .rtp entry.  See Chapter 
5 and the existing entries for format.

-Justin

>   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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-- 
==================================================

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

==================================================