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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Received on Sun Oct 01 2006 - 06:07:18 PDT
