On Thu, 2014-05-22 at 14:27 +0400, James Starlight wrote:
> One short question:
>
> after integration of the chromophore into the protein (making 2 peptide
> bonds of this residue with N and C termi of adjacent protein's residues)-
> I've noticed that total charge of my system has been decreased from 0 to
> -1. Assuming that both chromophore and protein had neutral charges why
> qtotal have been reduced after its joining ?
You should check your assumption. This should not happen, and to my
knowledge has never happened before. It is more likely that one of the
systems has a -1 charge (or another species you added to the unit has a
-1 charge) than you have encountered a bug that nobody has seen before.
You can use the "charge" command in tleap to quickly determine the
charge of any individual residue or atom in a particular unit. Type
"help charge" in tleap for more information.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 22 2014 - 04:30:02 PDT
