Hello,
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
residues.
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
apprciated.
khaled
Running: /Users/khaled/amber-build/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -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: /Users/khaled/amber-build/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
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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Received on Sun Jun 15 2008 - 06:07:23 PDT
