olymacfoogal at gmail.com
Thu Nov 18 13:27:04 CET 2010
You could use GLYCAM which is in AMBER so the parameters are already there
in the correct format (but not in the AMBER ported to GROMACS) and convert
that to GROMACS topology. It'll save you some time :)
I had problems converting the improper dihedral that holds the NAc group
planar using amb2gmx.pl so keep an eye on it.
On 15 November 2010 22:15, Anthony Cruz Balberdi <anthony.cruz5 at upr.edu>wrote:
> 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>
> > 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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