AMBER Archive (2009)

Subject: Re: [AMBER] Influence about HIS-HIE-HIS-HIP

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Apr 30 2009 - 09:27:02 CDT

On Thu, Apr 30, 2009, Rilei Yu wrote:
>
>  
> It is known that the default "leaprc" files assign the name HIS to
> HIE. I donot know wheather this change will introduce great influence
> to my MD simulation or not. You know an HIS is in the ligand binding
> pocket. So I believe there should be some influence to my protein
> complex simulation. Is there any tutorial than can guide me to assign
> the right from to the HIS. Namely, when will the HIS be use default
> form, and when will it be used as other forms such as HIP and HID?

The molprobity or reduce programs from Duke can help with this, as can several
programs on the web which are designed to predict pKa's of residues. You
might want to look at H++ (although other sites carry out similar
calculations):

  http://biophysics.cs.vt.edu/H++/

...dac

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