meng at cgl.ucsf.edu
Thu Jul 5 12:16:12 PDT 2012
To further elaborate, 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.
On Jul 5, 2012, at 11:57 AM, Elaine Meng wrote:
> 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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