Dear AMBER users,
I am trying to simulate an arsenic binding protein of 120 amino acids as
part of my PhD work. Arsenic will bind to three cysteine residues in the
protein. I have As(OH)3 coordinates and force fields. We have started the
MD and it is working well. As(OH)3 is moving and staying near to cysteine
residues during MD (so far 3 ns).
In reality, Arsenic will bind to the sulphur atoms of cysteine residues as
follows
As(OH3) + SH = As-S + H2O, Here SH means sulphur atom of the cysteine
residue.
Cys-S---AS---S-Cys
|
S
|
Cys
Bond length, bond angle and torsion angles are available. Now, I am trying
to create a force field for an Arsenic ion (3+) covalently linked with
sulphur atoms of cysteine residues. I have tried with antechamber but
ended up with an error like couldnot create MOPAC. I couldn't get any
success so far.
I will be very thankful, if anybody could kindly help me in this regard.
Thank you,
Sincerely
SHILPA T
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Received on Thu Mar 13 2014 - 23:30:02 PDT
