Dear AMBER users,
I've noticed the strange action of parmchk with improper torsions:
even for standard residue (RC for example) and ff99 parmchk found
missing improper parameters, that are listed below
parmchk -i RC.ac -f ac -o RC.frcmod
-p $AMBERHOME/dat/leap/parm/parm99.dat
(from the frcmod file)
IMPROPER
N*-CT-CM-C 1.1 180.0 2.0 Using default value
CM-N*-H4-CM 1.1 180.0 2.0 Using default value
CM-CM-HA-CA 1.1 180.0 2.0 Using default value
CA-CM-N2-NC 1.1 180.0 2.0 Using default value
C -N*-NC-O 1.1 180.0 2.0 Using default value
It looks like there is a problem with definition of improper torsions
in parmchk: the first atom should be in the third position (N*-CT-CM-C
-- CM-C-N*-CT). Any suggestions how to fix this problem would be
helpful.
With many thanks in advance,
Katya
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Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine
E-mail:kateryna_mirosh.ire.kharkov.ua
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Received on Wed Jan 04 2006 - 18:16:56 PST
