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

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Thu Feb 24 12:19:33 CET 2011

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)?

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?

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  

Sincerely Yours

Ruo-Xu Gu

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