[gmx-users] creating topology for ligand

[Justin Lemkul]

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

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

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

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