AMBER Archive (2005)Subject: RE: AMBER: Dihedral Energy calculation
From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Mar 02 2005  16:37:20 CST
Dear Yen,
> As Dr. Junmei has stated I am using
> 0.5 * Vn * (1 + cos(n*phi  gamma))
> Case I
> hcc3c o 1 0.80 0.0 1. Junmei et al,
> 1999
> hcc3c o 1 0.08 180.0 3. Junmei et al,
> 1999
> Case II
> c3c3nc 1 0.5 180.0 4. phi,psi,parm94
> c3c3nc 1 0.15 180.0 3. phi,psi,parm94
> c3c3nc 1 0.53 0.0 1. phi,psi,parm94
> If I encounter such atom types dihedral, should I
> i) consider(ALWAYS) all the 2 sets of parameter (Case
> I) and 3 sets (Case II).
Yes you should. So for case one each hcc3co dihedral term would considt
of the sum of two lots of the equation above. So if X is the dihedral angle
the contribution for each hcc3co set would be:
0.5*0.8*(1+cos(x0.0))+0.5*0.08*(1+cos(3x180))
And for case 2 each c3c3nc torsion set would be made up of a sum of 3
dihedral terms with the relevant parameters. Let me know if you can manually
match this up. If you find you are slightly off then email me directly and
we can go through an example.
> ii) since I am doing it manually and there is no
> problem of over counting 14 nonbonded interactions.
> Do the sign of the multiplicity(n) affect my
> calculation. What does the ve multiplicity signify.
The ve multiplicity has no effect of the energy since cos(x)=cos(x). So
since cos is a symmetric function so the n makes no difference  hence the
reason it is used as a marker for doing the 14NB calculation.
I hope this makes sense.
All the best
Ross
/\
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\oss Walker
 Department of Molecular Biology TPC15 
 The Scripps Research Institute 
 Tel: +1 858 784 8889  EMail: ross_at_rosswalker.co.uk 
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