On Wed, 18 May 2011, Piotr Wysoczański wrote:
> Brian you were right. It seems that I haven't copied my PRODRG nonbonded
> parameters to the OPLSX section. That actauly rises a question - how good
> are PRODRG generated parameters + another one: do the parameters across all
> CNS force-fields match with each other (talking still about non-bonded
> ones?)
You'll have to ask Daan va Aalten that one and then filter his response
through Michael Nilges for interpretation in the context of the 5.3
version of the CNS/ARIA forcefields! In general Michael's group & others
have worked hard to make the atom types that are covered in the current
versions of the parameter & topology files self consistent, so if your
modified residues contain atom types that are already represented in there
(and this is likely to be the case since PRODRG only supports N, C, O, S,
P, Cl, I, Br, F atoms, so unless you've got Cl, Br or F), then careful
consideration of the atom types should make it easy to choose appropriate
paramters from the existing entries.
Brian
--
Dr. Brian O. Smith ------------------------ Brian Smith at glasgow ac uk
School of Life Sciences, College of Medical, Vetinerary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
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