AMBER Archive (2006)

Subject: RE: AMBER: Antechamber : +ve charge species

From: Junmei Wang (
Date: Tue May 30 2006 - 10:31:07 CDT

You may run separately commands to find which step causes the problem.
First, convert a gout file to a mol2 file and check the mol2 file with a
software package such as sybyl etc (antechamber -fi gout -fo mol2 -i
test2.out -o test2.mol2 -at sybyl); Then, generate prepin file with bcc
charges (antechamber -fi mol2 -fo prepi -i test2.mol2 -o test2.prepin -c
bcc -nc 1). You use "-nc 1" to specify the net charge of your system.
Please send me the input file if you still have the problem.

All the best


-----Original Message-----
From: [] On Behalf
Of a a
Sent: Tuesday, May 30, 2006 5:04 AM
Subject: AMBER: Antechamber : +ve charge species

Dear Sir/Madam,

I am trying to run antechamber for a positive charged species (test2.out
an ESP calculation done by Gaussian). However, the following message
occurred. Is it because I should recompile the software or it means
that I
should only use antechamber for neutral compounds not +ve charged

[PATH]$ $AMBERHOME/exe/antechamber -i test2.out -fi gout -o test2.prepin
prepi -c bcc -s 2
Running: /PATH/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC -o

Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C

Running: /PATH/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC

Total number of electrons: 11; net charge: 0
Number of electrons is odd: 11
Please check the total charge and your -nc flag

Many thanks in advanced.......

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to