Hi, Gustavo,
In bondtype, Cl must have a valence of 1, this is why it gave a warning
message. You may first generate a mol2 or ac file (with resp charges)
and manually modify atom types/bond types if needed, then use prepgen to
produce a prepin file if prefer to.
Good luck
Junmei
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Gustavo Seabra
Sent: Friday, September 29, 2006 11:19 AM
To: amber.scripps.edu
Subject: AMBER: Problem using antechamber
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...
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 01 2006 - 06:07:19 PDT
