[gmx-users] creating topology for ligand

[neelam wafa]

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?

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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>
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