[MMTK] Amber parameters for ligands

Lars Skjærven larsss at gmail.com
Wed Nov 19 13:54:37 UTC 2008

Dear MMTK users,

I am looking into the possibilities of performing all atom NMA of a
protein with bound ligands using the Amber99 forcefield. In my case,
there is MgADP bound. Fortunately for me, Amber parameters for Mg2+
and ADP already exist in the Amber format (frcmod- and prep-file is
the common Amber format).

MMTK can nicely read the frcmod (parameter) file. Is there any methods
for reading the prep (topology) file as well? That is, to
automatically build the molecule file in MMTK/Database/Molecules from
the Amber prep file?

Am I correct that building the molecule file is all that needs to be
done in order to simulate with a ligand as long as the amber parameter
file (frcmod) is present?

Best regards,
Lars S.

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