[gmx-users] Constraint of active site in gromacs

[Raj D]

Thanks Justin . I will try it.
On May 7, 2015 5:48 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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