Re: AMBER: problems with Calcium ions treatment in GB run

From: David A. Case <>
Date: Thu, 28 Dec 2006 23:56:25 -0800

On Thu, Dec 28, 2006, Piotr Cieplak wrote:
> Apparently my calcium ions "C0" that have atom numbers: 2459, 2460, 2461
> are treated as "C" atoms in mdread.f of sander around line: 1200.

The surface-area facility in sander is based on the LCPO algorithm (see
references in the Users' Manual) and this only has parameters for the common
organic atoms and functional groups. Someone should step up to the plate
and program in a more general surface-area facility. Of course, it's not
clear that any surface-area model will make much sense for calcium ions

For now, turn on gbsa.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 31 2006 - 06:07:35 PST
Custom Search