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, Anthony On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA <[email protected]> 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 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
