AMBER Archive (2009)

Subject: [AMBER] NALA-ALA-CALA peptide with antechamber

From: Alan (alanwilter_at_gmail.com)
Date: Fri Apr 03 2009 - 11:33:17 CDT

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<<

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber