Guoxiong,
> Thank you for your reply. I will do as suggested to find a RESP
> charge for OPLS.
> Then how can I get the LJ parameters between those 'GAFF-particles'
> and 'OPLS-particles' since they are using two kinds of combine rules?
http://en.wikipedia.org/wiki/Benzonitrile
I would first try the simplest approach; and modify it if the box is
not correct...
if you decide to use the default Amber RESP approach (i.e. RESP-A1 in
the R.E.D. III.5 tools) for all your molecules, you could build a box
with vdW parameters from parm99.dat. Once you got your box, you study
its density, etc...
If you look at vdW param in gaff:
the atom types required for the nitrile group seems to be:
c1 12.01 0.360 Sp C
n1 14.01 0.530 Sp N
vdW parameters seem to be the same for n1/n3
c1 1.9080 0.0860 cp C
c3 1.9080 0.1094 OPLS
n1 1.8240 0.1700 OPLS
n3 1.8240 0.1700 OPLS
Consequently, I would first try to build a box for benzonitrile using
vdW param from amber99.dat and charges obtained with the default RESP
approach; then study the box to see how it goes...
or you decide to follow for all the OPLS approach...
regards, Francois
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Received on Tue Feb 21 2012 - 09:30:03 PST
