AMBER Archive (2009)

Subject: [AMBER] a method or program to try to guess the net charge of a small molecule

From: Alan (alanwilter_at_gmail.com)
Date: Fri Jun 26 2009 - 05:00:48 CDT

Hi List!

I use sometimes a step of antechamber with gasteiger just to try to guess
what
would be the net charge (usual, expected) of a small molecule, but
this fails or give the wrong value sometimes.
What I would like to know is if there's a method or program that would be
more
reliable or at least an alternative to cross check against
antechamber/gasteiger.

Using babel to convert a pdb to mol2 generates charges based on Gasteiger
method as well and so it has the same issues as mentioned for antechamber
above.

I know some (actually all) chemical compounds may have different net charges
depending on the environment (Ph), but the 'would-be' net charge at
physiological Ph would be fine enough, although probably the best way would
be a "chemistry expert" always near me, but I cannot ask that since I have a
DB of around 9000 small molecules for some which of them acpypi (a python
wrapper for antechamber developed here) is failing mainly because my script
is failing to guess the right net charge for the compound.

Many thanks in advance.

Alan 

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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