[gmx-users] DNA simulation

Luke Czapla czapla at rutchem.rutgers.edu
Thu Nov 28 20:45:21 CET 2002

Hi All,

  I am able to use the residues DADE for A and DTHY for T (etc), but some
of the hydrogens need to be added (some of the side chain ones on the
bases) and I was wondering if this can be done by modifying the hdb file.

  I am going to try to check the source code for pdb2gmx and try to make a
suitable workaround.  As far as uracil parameterization, John, I am
working in Wilma Olson's lab and we are quite enthusiastic about
parameterization of such things.  Maybe we could keep in touch, since I am
at Rutgers and in the same town and campus.  I know AMBER/CHARMM are
generally more suitable but there have been very good results with the
GROMOS87 force field and having open source code for GROMACS is very
promising since there is a lot of new ideas we have for force field
development which may be implementable and I'm considering my own GPL
fork of the source code if MD is the direction of my thesis research (DNA
-protein interactions is the big picture).

Luke Czapla

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