So, I have this tripeptide NALA-ALA-CALA (just a test case) for which
I use antechamber to generate the parameters with gaff and compare the
results with the one that Leap would do for it.
I found this little difference for dihedral involving the OC1 OC2 in CALA:
for gaff, the atomtypes and parameters are:
c3 o c o --> X -o -c -o 1.1 180. 2.
JCC,7,(1986),230 (in gaff.dat)
for Amber (e.g., 99SB), the atomtypes parameters are:
CT O2 C O2 --> X -O2-C -O2 10.5 180. 2.
JCC,7,(1986),230 (in parm99.dat)
I would like to have gaff matching the results for Amber99SB, but I
don't know if it is just something missing in gaff or it was done on
purpose.
Otherwise, one could add to gaff.dat something like:
c3 -o -c -o 10.5 180. 2.
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.
Cheers,
--
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<<
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Received on Sun Apr 05 2009 - 01:11:12 PDT
