AMBER Archive (2008)

Subject: AMBER: gasteiger is not working with ambertools 1.0

From: Alan (alanwilter_at_gmail.com)
Date: Mon May 19 2008 - 09:51:05 CDT

Hello!

To my despair, a simple command like:

antechamber -i dmp.pdb -fi pdb -o dmp_gas_sybyl.mol2 -fo mol2 -c gas
-s 2 -df 0 -at sybyl

Error message: The net charge of the molecule (-9999) does not equal
to the total charge (0.00 ) based on Gasteiger atom type, exit

is simply not working anymore. It was working pretty fine with antechamber 1.27.

dmp.pdb is a ligand from pdb 1BVG, case you want to test it yourself.
And, no, even using dmp.mol2, it doesn't work.

If -c bcc, things work fine.

And to my surprise, I found none of the tests released with ambertools
included -c gas.

I hope someone can help here.

Many thanks in advance.
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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