Sorry I just realize just writing C3 does not help as there are many C3
types in opls.info file depending on their chemical environment.
For example I was checking
CT "Thymine CH3-" (also similar CT ) for which
sigma epsilon
3.5000 0.08
But in opls_parm.dat CT has ( assuming it is the same CT)
sigma epsilon
1.8 0.06
So here it looks like just sigma/2 in amber (it should have been 1.75
instead of 1.8). But epsilon is different.
Regarding combination rule I read Dr. Case comments.
Prabal
On Tue, Feb 5, 2013 at 1:07 PM, Prabal Maiti <prabalmaiti.gmail.com> wrote:
> Hello,
> I was looking at amber12/dat/leap/parm dir for opls.info and opls_parm.dat
> I am confused about the vdw parameters? In the original OPLS file (
> opls.info) for example
> C3 has following
> sigma epsilon
> 3.905 0.175
> But same thing when put in amber (opls_parm.dat)
> sigma epsilon
> 2.00 0.15
> same for all other atom types.
>
> I thought in the opls_parm.dat it is 2^(1/6)*sigma/2. But it is not. Any
> idea what exactly is the scaling used? Also in AMBER one uses
> Lorentz-Bertelot combination in contrast to geometric combination in OPLS.
> How do we take into that while using OPLS in AMBER?
>
> Any suggestion welcome.
>
> Thanks
> Prabal
>
>
>
>
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Received on Tue Feb 05 2013 - 14:00:03 PST
