mirc...@sjtu.edu.cn wrote:
Dear All:
I am using GROMACS package to do molecular dynamics simulations under
OPLS_AA force field. I encounter some problems when preparing the
topology files of small molecules (ligands).My questions are as follows:
1, how to chose the atom type of each atom from the ligands?
2, how to define the charges of each atom? I know that, when the atom
type is defined, there will be a corresponding charge to this atom type.
Does it safe to use this charge in the simulations on the ligands (since
these charges are designed for amino acids)?
Proper parameterization is a difficult task. See, for instance:
http://www.gromacs.org/Documentation/How-tos/Parameterization
3,When the atom type and the charge of atom are defined, how to prepare
the file in the GROMACS format? Does there easier method to prepare such
files than manually?
There is at least one script (topolgen.pl) in the User Contributions section of
the Gromacs site, but it is not terribly intelligent and the resulting topology
should not be viewed as something that you should use without proper validation.
http://www.gromacs.org/Downloads/User_contributions/Other_software
Otherwise, break out Chapter 5 of the manual (something you should probably do
anyway) and your favorite text editor.
-Justin
Thank you very much for your time and your kindness. I really appreciate
if any one can share their experience in preparing the topology files
for ligands used under OPLS_AA force field and GROMACS package.
Sincerely Yours
Ruo-Xu Gu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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