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

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

303 Engel Hall
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Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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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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