ok thanks.

On 2 Mar 2018 22:25, "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> 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" <jalem...@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
>>>
>>> jalem...@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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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> Gromacs Users mailing list
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