AMBER: antechamber error

From: Ilyas Yildirim <>
Date: Sat, 17 Mar 2007 02:44:57 -0400 (EDT)

Dear All,

I have a structure, which has 54-55 atoms in it. I am trying to use
antechamber to assign the bond type/atom type info, but I am getting the
following error message (which I am not sure what it means):

antechamber -i part1_CH3_connect.pdb -fi pdb -o part1_CH3_connect.prepi
-fo prepi -c bcc -at gaff -nc 0 &
[1] 25421

Warning: the assigned bond types may be wrong, 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
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly
increase the computer time
Error: cannot run "/programs/amber9/exe/bondtype -i
judgebondtype() of antechamber.c properly, exit

[1] Done antechamber -i part1_CH3_connect.pdb
-fi pdb -o part1_CH3_connect.prepi -fo ...

The structure is neutral. I tried to google but could not find any useful
info on this error message. Any help is greatly appreciated. Thanks.


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
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Received on Sun Mar 18 2007 - 06:07:38 PDT
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