Dear Amber Users...
I am using OPLS-AA force field parameters for running simulations for ionic
liquid using Amber. I have some doubts regarding the preparation of the
dihedral part of the frc file using these OPLS parameters. I would use an
example to explain the doubt.
>From the paper JCTC (vol 5, 2009, pp 1038) I get the following information
for a particular dihedral
dihedral V1
V2 V3
NA-CA-CS-CS -1.788 0.756
-0.288
When I use these values in the amber frc file,
PK = V1/2 V2/2 V3/2
PN = -3, -2, 1
Is that right?
Now I have the following queries:
1) does a negative value of Vn imply a phase shift of 180deg?How do I
determine the phase shift?
2) Why are all the PK values in amber parm file positive and some in this
format negative?
3) How do I determine the IDIV factor. Should I determine them by
understanding how many torsions are there around that bond and divide PK by
that value? Or do the authors already take that into consideration and give
value for a single torsion (so in that case my IDIV factor will be one in
all cases)
Thanks for all the help
--
Debostuti Ghosh Dastidar
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Received on Wed Feb 20 2013 - 23:30:02 PST
