AMBER Archive (2009)

Subject: Re: [AMBER] Charge Problem

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Fri Aug 14 2009 - 03:55:07 CDT

Hi Bill,

        You need to correct the extra -0.8089 partial charge. This represents an
error and has no chemical meaning. From what you wrote, it seems reasonable
that this extra charge is coming from the modification made in the histidine
charges. At some point in the process, from incorporating the output of
R.E.D. into your model, you have introduce this error. (I am assuming that
you have executed R.E.D. to provided the correct overall -1 formal charge.) I
suggest that you go through each of your steps again and see where this extra
charge is added. This should give you ideas on how to correct the situation.

Cheers,
Karl

On Friday 14 August 2009 10:25, s. Bill wrote:
> Dear AMBER
> I have calculated the charge of my active site which contains on Zinc ion,
> three histidine and my inhibitor, using R.E.D. resp charge. and then
> assigned the new generated charged for the Imdiazol rings of His. But when
> I load my PDB file and check the charge of my system I found it is -1.8089
> (which should be -1 only). this difference returns to the new calculated
> charges for my active site. In this case, should I add only ONE Na+ ion,
> shouldn't I?
> I would appreciate any comment on this situation.
> Thanks in advance
> S. Bill
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