On Sat, May 16, 2009, Chih-Ying Lin wrote:
> How to setup the pH value?
> say, pH=5.0?
This depends *a lot* on what sort of behavior you are interested in.
You could assign side chains their most likely protonation states at pH5, and
keep them fixed. This would be a most common option.
Amber has a "constant pH" option, in which you just enter the pH as an input
option. But this is limited to implicit solvent simulations, and is still
pretty experimental. See the chapter in the Users' Manual on this, but be
prepared to proceed carefully and expect frustration. This is not yet an
option recommended for general use.
....hope this helps....dac
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Received on Wed May 20 2009 - 17:31:41 PDT
