Questions about Charmm22 ff

John Parkinson ECPT johnny at wadham.chem.ed.ac.uk
Thu Mar 12 11:16:08 EST 1998


Is anybody aware of any documentation on the charmm22 ff, I know the paper
is due to be published soon, but I was wondering if there were any other
sources of information on it. In particular a description of the IC
topology statement would be useful.
One thing that has been puzzling me for some time is the ff's ability (or
inability) to model h-bonds. From the Xplor manual, I understand that the
latest ff's do not need an explicit H-bond term and that the Charmm22 ff
includes H-bond parameters for analysis only. Fine. However, when I try
running a dynamics simulation of camphor in the enzyme P450, the camphor
is found to tumble contrary to experimental data in which a H-bond is
thought to be responsible for tethering the camphor within the binding
pocket.

People using the AMB*R ff to simulate the process get around the tumbling
behaviour by artifically increasing the van-der waals contributions. This
also works for Charmm22, but seems a bit of a cop out to me. Any
suggestions ?

John Parkinson

Edinburgh Centre for Protein Technology
Joseph Black Chemistry Building, The King's Buildings
West Mains Road, Edinburgh EH9 3JJ, UK




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