AMBER: Problem using antechamber

From: Gustavo Seabra <>
Date: Fri, 29 Sep 2006 12:19:12 -0400


I'm trying to use antechamber to generate parameters for ClO4-.

I used the following procedure:

1. from a pdb file, create a gaussina input using antechamber:
$ antechamber -i PCL-.pdb -fi pdb -o -fo gcrt -nc -1

2. Run the gaussian calculation

3. Use antechamber to generate the prepin file. Here's where I get the

$ antechamber -i pcl-.log -fi gout -nc -1 -rn pcl- -o pcl-.prepin -fo prepi
-c resp

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 "/scr/arwen_2/seabra/amber10/exe/bondtype -i
judgebondtype() of antechamber.c properly, exit

Am I doing something wrong here?



P.S.: I know that the parameters for this ion are available in the Amber
parameter database. I'm trying to learn here...

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 01 2006 - 06:07:18 PDT
Custom Search