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
Astrid
----- Ursprüngliche Mail -----
Von: "Ouaray Z." <zo1g10.soton.ac.uk>
An: amber.ambermd.org
Gesendet: Montag, 21. März 2011 14:52:23
Betreff: [AMBER] protein charge
Hi,
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?
Thanks.
Z.O
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Dr. Astrid Maass
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Received on Mon Mar 21 2011 - 07:30:03 PDT
