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 |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 17 2009 - 01:08:40 PDT
