[AMBER] charges for ion and surrounding residues at the active site

From: Jorge Iulek <jiulek.ig.com.br>
Date: Mon, 19 Mar 2012 21:33:10 -0300

Dear all,

     I have a protein to which I wanted to make some molecular dynamics
and co-factor binding energy calculations. Nevertheless, the active site
has a Calcium ion. I refer to i) J Mol Biol. 2007 February 16; 366(2):
687701; ii) Journal of Structural Biology Volume 157, Issue 3, March
2007, Pages 444453; iii) J Chem Phys. 2010 Apr 7;132(13):131101; which,
in general, suggest that more properly the charges for the ion and the
surrounding residues (including the co-factor?) should be improved with
a QM calculation beforehand. Also, I see the tutorials a)
http://people.sissa.it/~raugei/lecture_notes/amber.pdf ; b)
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php and c)
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php . As far as I
understand, I should submit to a QM program an excerpt of the protein,
id est, the ion and the closest (complete to the N and C=O) residues
(maybe any residue which is within 6 A from the ion - so I have a
molecular fragment(s)) and then get from the QM program the modified
parameters for them all (including charges). What I could not figure
still clearly is a step by step tutorial to do this. For this kind of
molecular fragment (ion + surrounding residues - which most are not
connected to each other) might the tutorial
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php fulfill all
requirements? In this case it does not resort to Gaussian, should this
be enough to parametrize the residues and ion to be incorporated into
the force filed and do the dynamics? I would be happy to read further
references and tutorial on how to do this.

Jorge

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Received on Mon Mar 19 2012 - 18:00:02 PDT
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