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
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
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.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Mar 18 2007 - 06:07:38 PDT
