AMBER Archive (2007)

Subject: Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat?

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Sat Mar 10 2007 - 01:37:06 CST

I get it. Thank you very much.

On 3/9/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> look at the Amber web site under "file formats". it explains this file and
> what the numbers are.
>
> On 3/9/07, Chengwen Chen <chenchengwen_at_gmail.com> wrote:
> > Dear Amber users,
> >
> > I would like to get the van der Waals parameters and 6-12 potential
> > parameters of NB in parm99.dat. But I can't find these parameter after
> "MOD4
> > RE". And there are some atom type including NB is listed before "MOD4
> RE".
> > What does that mean? How can I get the parameter I wanted?
> >
> > Thank you very much
> >
> >
> >
> > from parm99.dat
> >
> > N NA N2 N* NC NB NT NY
> > C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ
> >
> > MOD4 RE
> > H 0.6000 0.0157 !Ferguson base pair geom.
> > HO 0.0000 0.0000 OPLS Jorgensen,
> > JACS,110,(1988),1657
> > HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
> > HC 1.4870 0.0157 OPLS
> >
> >
> > Best Wishes,
> >
> > Chen Chengwen
> >
> >
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