AMBER Archive (2006)

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

From: Junmei Wang (jwang_at_encysive.com)
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

Junmei
 

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

Dear Sir/Madam,

I am trying to run antechamber for a positive charged species (test2.out
is
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
species:

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

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
-p
gaff

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.......

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