AMBER Archive (2009)

Subject: RE: [AMBER] mean of character in frcmod.ff03

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 15 2009 - 09:58:31 CDT

Hi Quan,

> I want add a parameters of torsion in frcmod.ff03, but I don't
> know the exact means of the character of second，third and forth
> colums：
>
> CT-CT-C -N 1 0.0000 0.0 -4.
> CT-CT-C -N 1 0.0560 0.00 -3.
> CT-CT-C -N 1 0.0657 180.00 -2.
> CT-CT-C -N 1 0.7784 180.00 1.

You should check the original Cornel et al JACS 95 paper for an explanation
of this.

Edih = sum(1,ndih)(Vn/2)(1+cos(n theta - phi))

Column 1 defines the atom types making up the dihedral. Column 2 is a
divisor on the barrier height that is used in cases where there are wild
types for the 1st and 4th atom. To avoid confusion NEVER user wild type
definitions and always set this value to 1. Column 3 is (Vn/2), column 4 is
the phase (phi) and column 5 is the periodicity n. The - sign is used to
show that more than one periodic term is expected. I.e. if you have multiple
dihedral terms with the same atom types but different periodicities set
column 5 negative for all but the last one.

You can also see this page: http://ambermd.org/formats.html#parm.dat

Under section 6.

Good luck,
Ross

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|\oss Walker

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| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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