[AMBER] antechamber error

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Wed, 24 Aug 2011 10:03:57 +0530

Dear Amber users,
Thanks for your help and suggestions earlier,
I'm getting the following error while using antechamber to generate prepin
file from pdb file for the ligand. I'm using amber11.

The same command was working nicely with amber10. The prepin file is
generated correctly if I use other charges like "Gasteiger charges".
But I wanted to stick to the bcc charge as I had done for other ligands
using amber10.
Should the difference in charges (bcc vs gas) affect the result in
simulation that I'm going to perform later and calculate free energy using
MMPBSA?


Errors with antechamber: 

----
[vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69.prep -fo
prepi -c bcc -s 2
Running: /opt/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /opt/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 280; net charge: 0
Running: /opt/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/opt/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in
charge.c properly, exit
----
[vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69.prep -fo
prepi -c gas (working...)
-- 
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Aug 23 2011 - 22:00:02 PDT
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