[Chimera-users] AMBER99SB

[Nikolay Igorovich Rodionov]

Thank you Elaine, do polarizable force fields offer an advantage over fixed charge over forcefields when looking at surface interactions on solvated protein multimers?  
Also, is the new release stable? I think I'll give it a try. Thanks for keeping Chimera up to date!

Nikolay Rodionov

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, July 05, 2012 1:57 PM
To: Nikolay Igorovich Rodionov
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] AMBER99SB

Hi Nikolay,
Fixed charge.  The polarizable ones have "pol" in their names.

I should mention that Chimera 1.7 (development, daily build version) has been updated to use Ambertools 12, including newer force fields.  The default force field in Chimera 1.7 is ff12SB. For all the gory details, one should consult the Amber documentation, but there is some information here:

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#standard>
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco



On Jul 5, 2012, at 11:33 AM, Nikolay Igorovich Rodionov wrote:

> Hi all,
>  
> I just have a quick question. Is AMBER99SB a fixed charge or polarizable forcefield?
>  
> Thank you,
> Nikolay Rodionov