AMBER Archive (2009)

Subject: Re: [AMBER] Charge Problem

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Aug 15 2009 - 07:06:45 CDT

Dear Bill,

> 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.

As Karl told you, there is a problem in your system. You should have
an integer value for your system (integer means integer +/- .0005 max
error). However, this is strongly related to the constraint(s) you
used during the fitting step for your system (If this(these)
constraint(s) are not integer it is normal the total charge of your
system is not an interger).

This is difficult to help you without having more information: May be
you could send us the P2N file(s) of your bio-organometallic system.

regards, Francois

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