AMBER Archive (2009)

Subject: [AMBER] antechamber and wrong net charge with gasteiger method

From: Alan (alanwilter_at_gmail.com)
Date: Tue Apr 14 2009 - 12:41:30 CDT

Hi there,

So I have this peptide (gly-hip-gly) for testing purpose, attached
(mol2 and pdb file).

The net charge is +1. However, if I try:

antechamber -i agJJJ.mol2 -fi mol2 -o agJJJ_bcc_gaff.mol2 -fo mol2 -c bcc -nc 0

Info: Bond types are assigned for valence state 3 with penalty of 1
Total number of electrons: 143; net charge: 0
INFO: Number of electrons is odd: 143
      Please check the total charge (-nc flag) and spin multiplicity (-m flag)

or:

antechamber -i agJJJ.mol2 -fi mol2 -o agJJJ_gas_gaff.mol2 -fo mol2 -c gas -nc 1

Info: Bond types are assigned for valence state 3 with penalty of 1
The net charge of the molecule (1) does not equal to the total charge
(0.00 ) based on Gasteiger atom type, exit

I don't know how 'gasteiger' method was implemented in antechamber,
but this output is not correct.

And yes, '-c bcc -nc 1' works fine.

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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