AMBER Archive (2009)

Subject: [AMBER] zwitterionic form of ARG and antechamber

From: Alan (alanwilter_at_gmail.com)
Date: Mon Apr 06 2009 - 07:33:31 CDT

Hi there,

So I have a single ARG in a pdb file in zwitterionic form and I am
playing with antechamber.

If I do (bcc):
----------------------
antechamber -i arg.mol2 -fi mol2 -o new.mol2 -fo mol2 -c bcc -nc 1

Info: Bond types are assigned for valence state 2 with penalty of 1

Total number of electrons: 94; net charge: 1

Running: /Users/alan/Programmes/amber10/bin/mopac.sh
----------------------
All fine

But, if I do (gasteiger):
----------------------
antechamber -i arg.mol2 -fi mol2 -o new.mol2 -fo mol2 -c gas -nc 1

Info: Bond types are assigned for valence state 2 with penalty of 1

The net charge of the molecule (1) does not equal to the total charge
(1.00 ) based on Gasteiger atom type, exit
----------------------
Failed. Note that, for some reason (probably re rounding numbers), (1)
not equal (1.00).

Looking at charge.c, line 723:

TotalGasCharge += gas[gasparmindex[i]].charge;

It seems that TotalGasCharge is accumulating a decimal residue that
shouldn't be there.

BTW, wouldn't be better to round anyway TotalGasCharge to the closest
integer, since in the end antechamber will only pick integer values
for net molecular charge?

Cheers,
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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