[Chimera-users] AMBER99SB

[Elaine Meng]

Hi Nikolay,
You're welcome -- we try to answer what we can!

As mentioned a few days ago, even if you choose in Chimera to add charges from the polarizable force field, it only adds the fixed parts of the charges.  The main purpose of doing that would be then to write out prmtop and crd files for further polarizable calculations in Amber itself.  You cannot do polarizable calculations in Chimera, sorry.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#standard>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-July/007747.html>

I hope this clarifies,
Elaine
----------
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 9, 2012, at 10:27 AM, Nikolay Igorovich Rodionov wrote:

> Hi Elaine,
> 
> First off, I would just like to say thank you. I'm just realizing how often I seek out this mailing list for help and how often you steer people in the right direction. Thanks so much!
> 
> I've been reading about polarizable forcefields and I have a question on applying the AMBERff03.r1 polarizable force field in Chimera. From what I understand of polarizable forcefields thus far is that their net force calculations are more accurate because the factor in polarization of molecules when they are surrounded by a solvent with a high dielectric constant, such as water.
> 
> When I applied the force field on two test molecules, both the same protein but one being solvated, the calculated charges stayed the same. In theory, shouldn't have the presence of water slightly altered the charges? Chimera's force field application tool does not let you input environment parameters such as the dielectric constant. Is Chimera automatically set up for water solvation or is there some flaw in my understanding of pol.ff? 
> 
> Thanks,
> Nikolay Rodionov
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: Thursday, July 05, 2012 3:28 PM
> To: Nikolay Igorovich Rodionov
> Cc: chimera-users at cgl.ucsf.edu BB
> Subject: Re: [Chimera-users] AMBER99SB
> 
> Hi Nikolay,
> 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.
> Elaine
> 
> 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:
>> 
>> <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
>> 
>> 
>> 
>> 
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> 
> 
> 
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