AMBER Archive (2006)

Subject: AMBER: Antechamber : +ve charge species

From: a a (patd_2_at_hotmail.com)
Date: Tue May 30 2006 - 05:04:05 CDT

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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