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

From: David A. Case <>
Date: Wed, 19 Mar 2008 08:42:13 -0700

On Thu, Mar 06, 2008, Edyta Malolepsza wrote:
> Some chemically equivalent atoms (oxygen atoms in COO- for ASP and GLU
> and for all terminal COO- or hydrogen atoms in NH2 for ASN and GLN)
> seem to be not equivalent in AMBER9.
> 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.)

> After including frcmod file with new order of atoms for IMPROPER it
> was always applied to prmtop file only for first COO- group in the
> system.

I've entered this on bugzilla:

We'll try not to forget about it! Thanks for the report.....dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:12:18 PDT
Custom Search