Hi, Ross,
Thanks very much for you detailed explanation!
quan
> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
> Subject: RE: [AMBER] mean of character in frcmod.ff03
> Date: Wed, 15 Apr 2009 07:58:31 -0700
>
> 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
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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Received on Fri Apr 17 2009 - 01:11:25 PDT
