Re: [AMBER] Regarding "Total unperturbed charge: -0.507900" on CYP1A1

From: <>
Date: Wed, 13 Jul 2011 16:26:07 -0400 (EDT)


> I have prepared the protein-Heme-substrate complex. After adding TIP3
> WaterBox, the whole system is showing "*Total unperturbed charge:
> -0.507900
> *".
> Can you please suggest me, whether I shall proceed with -0.507 charge on
> protein complex or with ~ +0.5 charge by adding one Na+ ?

this message is an indication that something went wrong during your system
setup, most likely connected to the heme parameters or linkage to the
protein. A non-integer charge system makes no sense to simulate in my
opinion, as it does not correspond to a physically existing state. I would
investigate if your partial charges are really assigned ok.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Jul 13 2011 - 13:30:04 PDT
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