AMBER Archive (2008)

Subject: Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 19 2008 - 17:54:24 CDT

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

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