Dear Amber community!
Learning guanosine parametrization in ff99, I've been confused with one
observation about impropers.
To extract guanosine parameters I've done the follows:
1)creating Mol2:
tleap -s -f leaprc.ff99SB
savemol2 DGN dgn.mol2 1
2)extracting params:
parmchk -i dgn.mol2 -f mol2 -o dgn_params.frcmod -p
/home/nilov/amber10/dat/leap/parm/parm99.dat -a Y
I was surprised that there is no improper fixing NH2 group of guanosine in
obtained dgn_params.frcmod among improper section:
IMPROPER
CB-CK-N*-CT 1.0 180.0 2.0
H5-N*-CK-NB 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
C -CB-CB-NB 1.1 180.0 2.0 Using default
value
CB-NA-C -O 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)
C -CA-NA-H 1.0 180.0 2.0 General improper
torsional angle (2 general atom types)
N2-NA-CA-NC 1.1 180.0 2.0
CB-N*-CB-NC 1.1 180.0 2.0 Using default
value
Basing on atom types, aminogroup of guanosine could be represented as
H
/
-CA-N2
\
H
There is improper
X -X -N2-H 1.0 180. 2. JCC,7,(1986),230
with general atom types in parm99.dat, so I don't understand why CA-H
-N2-H is absent in frcmod.
Thanks in advance!!
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Tue Jun 22 2010 - 03:30:03 PDT
