Re: [AMBER] chlorine naming question and parametrization

From: Jason Swails <>
Date: Thu, 1 Dec 2011 22:29:08 -0500

On Tue, Nov 29, 2011 at 2:53 PM, Andrew Voronkov <>wrote:

> This record is recognized as chlorine, but not in Amber:
> ATOM 3373 CL1 RES 211 15.775 50.075 17.009 1.00 0.00
> CL

The problem is that the topology file does not store element information (a
limitation, IMO), so it has to guess based on the atom name (and mass, in
the case of sqm). However, ambpdb doesn't use the mass, it just uses
names. That's probably why you don't think Amber is considering your
chlorine a Chlorine atom.

However, element identity is unimportant in classical mechanics, since the
classical equations only care about total mass and partial charge (how many
electrons an atom has and how many of the nucleons are protons are

You could check the parameters (i.e. the mass, charge, etc.) on the atom to
see if they seem sensible. rdparm is useful here.


> Best regards,
> Andrew
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Dec 01 2011 - 19:30:02 PST
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