[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 24 12:42:57 CET 2011

mircial at 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:


> 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.


Otherwise, break out Chapter 5 of the manual (something you should probably do 
anyway) and your favorite text editor.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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