AMBER Archive (2009)
Subject: [AMBER] NALA-ALA-CALA peptide with antechamber
From: Alan (alanwilter_at_gmail.com)
So, I have this tripeptide NALA-ALA-CALA (just a test case) for which
for gaff, the atomtypes and parameters are:
for Amber (e.g., 99SB), the atomtypes parameters are:
I would like to have gaff matching the results for Amber99SB, but I
Otherwise, one could add to gaff.dat something like:
Or introduce atomtype o2 in gaff.dat, which doesn't exist yet.
Pardon, if I sound not clear since in part I am thinking aloud.
Any comments would be very appreciated.
-- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<