You might not use pdb2gmx for such task.
Once you have generated topology in AMBER format with Antechamber in
GAFF, you will need to use some tools like ambconv.pl or ambconv (one is
Perl script and one is a C++ programme, check GROMACS' website) to
convert those files into GROMACS format.
There is ffamber, a port for AMBER force field to GROMACS, which largely
similar to what ambconv.pl or ambconv produces. They will provide force
field for protein and nuclei acids through pdb2gmx. With some
hand-modifications to the files, you can combine ambconv and ffamber, so
you have a solution for almost all molecules.
Regards,
Yang Ye
Xiangyu Fan wrote:
Hi all,
I am using GAFF force field for Gromacs package to simulate MD of
surfactant molecule. I know we can generate .top file using some
simple command like pdb2gmx if we use gromos force field. I am just
wondering whether I can do the similar thing when using GAFF force
field. If you have any experience in GAFF+Gromacs, please give me some
advice. thanks
Xiangyu Fan
UNC-Chapel Hill
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