[gmx-users] Help needed on using general amber force field (GAFF) in Gromacs

Yang Ye leafyoung at yahoo.com
Fri Mar 14 05:30:27 CET 2008

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.

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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