On Wed, Mar 19, 2008, Edyta Malolepsza wrote:
>
> It can be done also by reordering atom positions in topology file
> without any code or energy formula change. I have written program in
> python which reads original topology file and AMBER libraries for
> amino acids and nucleic to create new topology file with correct order
> of atoms for IMPROPER's. With new topology file any permutations of
> equivalent atoms give the same results - potential is symmetric.
Is it possible to revise the libraries so that the "symmetric" prmtop file is
made in the first place?
I hope one of the Amber "force field people" has the time to jump in here, as
I cannot take on any new responsibilities right now.
...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:12:24 PDT
