AMBER Archive (2008)

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

From: Edyta Malolepsza (
Date: Wed Mar 19 2008 - 11:49:45 CDT

Dear David,

> > The reason can be in order of atoms in IMPROPER angles for NH2 and COO- groups.
> This will only really be fixed by a change in the way the impropers are
> defined, I think. Someone will have to take this on as a project; it will
> be easier once we implement the CHARMM force field equations (but don't hold
> your breath.)

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.

I can share this program, please let me know if somebody is interested.

With best regards,

Edyta Malolepsza
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