Dear all,
I tried checking the GAFF for a molecule generated by Antechamber using parmchk and parmchk2
I get very different values of the potential barrier - please see below
how to judge the quality of the parameters from the scoring penalty - given that improper dihedral scoring is of the order of 6-42 compared to normal dihedral ?
Thanks
Fatima
from parmchk:
DIHE
h5-cc-ss-ca 1 1.100 180.000 2.000 same as X -c2-ss-X
nd-cc-ss-ca 1 1.100 180.000 2.000 same as X -c2-ss-X
ca-ca-cc-cd 1 0.700 180.000 2.000 same as X -c2-ca-X
ca-ca-cc-ss 1 0.700 180.000 2.000 same as X -c2-ca-X
ca-cc-ss-cc 1 1.100 180.000 2.000 same as X -c2-ss-X
cc-ss-cc-nd 1 1.100 180.000 2.000 same as X -c2-ss-X
cc-ss-cc-h5 1 1.100 180.000 2.000 same as X -c2-ss-X
cd-cc-ss-cc 1 1.100 180.000 2.000 same as X -c2-ss-X
from parmchk2
DIHE
h5-cc-ss-ca 2 2.200 180.000 2.000 same as X -c2-ss-X , penalty score=232.0
nd-cc-ss-ca 2 2.200 180.000 2.000 same as X -c2-ss-X , penalty score=232.0
ca-ca-cc-cd 4 2.800 180.000 2.000 same as X -c2-ca-X , penalty score=232.0
ca-ca-cc-ss 4 2.800 180.000 2.000 same as X -c2-ca-X , penalty score=232.0
ca-cc-ss-cc 2 2.200 180.000 2.000 same as X -c2-ss-X , penalty score=232.0
nd-cc-ss-cc 2 2.200 180.000 2.000 same as X -c2-ss-X , penalty score=232.0
h5-cc-ss-cc 2 2.200 180.000 2.000 same as X -c2-ss-X , penalty score=232.0
cd-cc-ss-cc 2 2.200 180.000 2.000 same as X -c2-ss-X , penalty score=232.0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 07 2015 - 06:30:03 PDT
