COnversion of x-plor parameters to AMBER format

David Konerding dek at socrates.ucsf.edu
Sun Nov 17 23:42:38 EST 1996


Hi, x-plorers:

I've got some X-PLOR parameters (bond angles, lengths, and dihedral/improper
angle) that I would like to convert to AMBER format.    This is a straightforward
process for angles and lengths, which can be converted easily.  

However, I'm having more trouble with the dihedral and improper angles.  Basically,
I cannot find any documentation in the X-PLOR manual about the format of the
parameter files, specifically with respect to the ordering of atom names in
impropers and the meaning of the values in teh columns to the right of the atom names:

For example: 
 improper  HA   NH1  CT   CUA1     $kchi    0   65.977
 dihedral  HA   CUA1 CUA1 C        $kdih    3    0.0

Is the atom name ordering for impropers in X-PLOR identical to AMBER?
(IE, I J K L = 
                     I
                     K
                   J   L  (I think that's AMBER's ordering, but I can't recall at the moment)

And for dihedrals/impropers, is the value after the force constant the multiplicity?

THanks,

-- 
--------------------------------------------------------------------------------
Email: dek at cgl.ucsf.edu    David Konerding     WWW: http://picasso.ucsf.edu/~dek
--------------------------------------------------------------------------------
Snail: Graduate Group in Biophysics
Medical Sciences 926, Box 0446
University of California
San Francisco, CA 94143



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