AMBER Archive (2008)

Subject: AMBER: Coordinated Zinc

From: Khaled Barakat (
Date: Wed Jun 11 2008 - 14:29:18 CDT


I am trying to use Antechamber to create a prepin file for a zinc ion coordinated with 3 cysteine
residues and 1 histedine.
I created a pdb file (attached) for the 4 residues and the zinc ion. the N terminals are capped for the
I am trying to take the charges and the bond parameters from this file in order to modify my system.

the command i used is:

antechamber -i p5-out.pdb -fi pdb -o p5-out.prepin -fo prepi -c bcc -s 2

I always get this error (see under signature). I do not know what is wrong with that. any help will be

Running: /Users/khaled/amber-build/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -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: /Users/khaled/amber-build/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o

Total number of electrons: 334; net charge: 0

Running: /Users/khaled/amber-build/amber8/exe/divcon
Unable to find mopac charges in divcon.out

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