AMBER Archive (2005)

Subject: AMBER: Antechamber error

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Oct 25 2005 - 18:27:39 CDT

Dear Amber users,
  When I run antechamber to prepare *.prepin file, I say:

antechamber -i dag2.pdb -fi pdb -o dag.prepin -fo prepi -c bcc -s 2

It says:

*****************
Running: /sprog/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 358; net charge: 0

Running: /sprog/amber8/exe/divcon

Running: /sprog/amber8/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p
/sprog/amber8/dat/antechamber/BCCPARM.DAT -j 4

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
******************

I checked my structure for valency and bond requirements. Everything
seems fine.
 So it does not make sense to adjust the valence penalty parameters or
increase MAXVASTATE.

I am attaching my PDB file.
Has anyone encountered this problem before?
Any help woud be greatly appreciated.
thanks
Nitin
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