meng at cgl.ucsf.edu
Thu Jul 5 12:27:52 PDT 2012
The force field discussion is really beyond the scope of this forum. Maybe you could ask on the Amber forum, or try searching the literature. However, as mentioned earlier today, if you are doing analysis in Chimera only, it would only be using the fixed parts of the charges no matter which force field you choose.
The daily build is literally a daily build, so no, it is not stable, it will change essentially daily. If you meant is it usable or does it crash, I would say it is very usable most of the time. However, on some small proportion of days it may misbehave in noticeable ways. I keep multiple versions of Chimera, the last production release plus one or more recent daily builds.
On Jul 5, 2012, at 12:04 PM, Nikolay Igorovich Rodionov wrote:
> 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:
> 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
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