[gmx-users] Parameterization

Anthony Cruz Balberdi anthony.cruz5 at upr.edu
Mon Nov 15 23:15:57 CET 2010

Dear Yuvraj:

There is a protocol to find the charges and force field parameters for
new molecules for the AMBER force field. The best way is to try to
find the parameters from a publication. If you dont find anything then
use RED to find the charges (http://q4md-forcefieldtools.org/RED/).
Then use ambertools to find the necessary force field parameters and
generate an AMBER topology. After that use acpype to transform the
amber topology to a GROMACS topology. From the GROMACS topology the
create an itp file to use in your GROMACS TOPOLOGY.

To better understand what I said please read the reference for the
force field, the GROMACS manual and the RED tutorial.

Best Regards,


On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA <yuvrajthedon at gmail.com> wrote:
> How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER
> force field to use in GROMACS.
> Please suggest some solutions.
> Thanks
> --
> Yuvraj
> --
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