Dear Amber users,
I am currently working on AM1-BCC charge computation by the antechamber module of amber.
I seem to have a problem with charge computation.
My molecule has a zero charge.
here is the antechamber chamber command I use
antechamber -s 2 -i t1.mol2 -fi mol -o mol.mol2 -fo mol2 -at gaff -c bcc -nc 0 -m 1 -rn MOL -j 4
Running: /usr/local/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 0; net charge: 0
Running: /usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
here is the error message in the sqm.out :
QM ATOM VALIDATION: nquant has a value of 0
which is bigger than natom of 0. Need 0 < nquant <= natom.
SANDER BOMB in subroutine validate_qm_atoms
nquant illegal
Need 0 < nquant <= natom
Is there a bugfix or workaround for the problem above?
Regards,
Cenk Andac, M.S., Ph.D.
Asst. Professor of Medical Pharmacology
Department of Medical Pharmacology
School of Medicine, Mevlana University, Konya
Turkiye 42003
Cell: +90-(536)-4813012
E-Mail:cenk_andac.yahoo.com
Web : http://med.mevlana.edu.tr/personel.asp?ID=1
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Received on Sun May 19 2013 - 11:30:04 PDT
