Re: [AMBER] protein charge

From: Astrid Maaß <>
Date: Mon, 21 Mar 2011 15:23:04 +0100 (CET)

Hi Z.O,

when I count the charges of your protein I find 25 positively charged standard residues (ARG + LYS, no HIP) and 19 negatively charged ones (GLU, ASP), yielding your expected net charge of +6. However there appear to be three non-standard residues present: deprotonated, i.e. negatively charged cysteine (CYM, surrounding a Zn-atom). These could account for the observed lower net charge of +3.

Kind regards

----- Ursprüngliche Mail -----
Von: "Ouaray Z." <>
Gesendet: Montag, 21. März 2011 14:52:23
Betreff: [AMBER] protein charge


i have to do modelisation on the following protein. But i have a problem with the charge assignement on my protein by Amber.
the tleap check of the protein says that the protein is +3. But when i manually count the charge i find +6.
did somebody had the same problem? if yes, how to fix it?


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Dr. Astrid Maass
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Schloss Birlinghoven
D-53754 Sankt Augustin, Germany
Phone: +49 - 2241 - 14 - 2481
Fax:   +49 - 2241 - 14 - 2181
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Received on Mon Mar 21 2011 - 07:30:03 PDT
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