AMBER Archive (2006)

Subject: AMBER: Problem using antechamber

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Sep 29 2006 - 11:19:12 CDT

Hi,

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 pcl-.com -fo gcrt -nc -1

2. Run the gaussian calculation

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

$ 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
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit

Am I doing something wrong here?

Thanks!

Gustavo.

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

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