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
package.
Sincerely Yours
Ruo-Xu Gu
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