[gmx-users] creating topology for ligand
jalemkul at vt.edu
Thu Mar 1 14:14:27 CET 2018
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
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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