Re: [AMBER] Further question on protonation state of histidine

From: David A Case <>
Date: Fri, 6 Apr 2012 09:28:59 -0400

On Fri, Apr 06, 2012, Acoot Brett wrote:
> Even for high resolution structure of protein, the protonation state of
> HIS is usallly unclear or unspefified. Do we have some rules to correct
> the protonation state of the residues including HIS? Or there is a
> server for this purpose?

What leap does by default is determined by your leaprc file; all of the
standard leaprc files use HIE by default. But it is recommended that you
examine each residue and not rely on the default. The reduce program (now
included in AmberTools) can help, as can the "H++" program on the web. Other
tools for estimating protonation states exist--these are just the ones I am
most familiar with.


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Received on Fri Apr 06 2012 - 06:30:21 PDT
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