[gmx-users] creating topology for ligand

[Justin Lemkul]

On 3/2/18 12:18 PM, neelam wafa wrote:
> Thanks Justin
>
> Can you please suggest me any article or reading that can help me to
> understand the factors to be considered while choosing a force field or to
> parameterize the ligand?

I could suggest hundreds. Start with even a basic Google search for MD 
force field review papers, references in the GROMACS manual for each of 
the force fields, etc.

-Justin

> On 1 Mar 2018 18:14, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>> On 3/1/18 8:03 AM, neelam wafa wrote:
>>
>>> Dear gmx users
>>>
>>> I am trying to run a protein ligand simmulation. How can i create topolgy
>>> for ligand. prodrg topology is not reliable then which server or software
>>> can be used?  can topology be created by T LEEP off ambertools package for
>>> gromacs??
>>>
>> The method you use depends on the parent force field you've chosen. The
>> PRODRG and ATB servers are for GROMOS force fields, GAFF methods (RED
>> server, antechamber, etc) are for AMBER. ParamChem/CGenFF are for CHARMM.
>> You can't mix and match. You need to do your homework here to make sure
>> that the force field you've chosen for your protein is an appropriate
>> model, as well as whether or not you can feasibly parametrize your ligand
>> (not an easy task and generally not advisable for a beginner, because you
>> should *never* trust a black box and always validate the topology in a
>> manner consistent with the parent force field).
>>
>> secondly how to select the boxtype as I am new to simmulation so cant fix
>>> the problem.  Please also guide me what factors should be considered to
>>> select the water model??
>>>
>> The water model is part of the force field; each has been parametrized
>> with a particular model (though some do show some insensitivity if changed,
>> but again this is your homework to do before ever thinking about doing
>> anything in GROMACS or any other MD engine).
>>
>> The box shape has no effect as long as you set up a suitable box-solute
>> distance that satisfies the minimum image convention. You can use non-cubic
>> boxes to speed up the simulation if it's just a simple protein (complex) in
>> water.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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