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 - 10:42:13 CDT

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:

   http://bugzilla.ambermd.org/show_bug.cgi?id=47

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

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