Dear sir:
I want to use antecamber to establish the small molecule---SAM,
however, when I input the conmmand
antechamber -i sam.pdb -fi pdb -o sam.mol2 -fo mol2 -c bcc
something is wrong
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 PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time
Error: cannot run "/opt/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
I have upload my pdb file, please help me to solve the problem
Thank you for your patient
Your sincerely
Zhou Gong
Biomolecular Physics and Modeling Group
School of Physics
Huazhong University of Science and Technology
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- application/octet-stream attachment: sam.pdb
Received on Wed Dec 08 2010 - 07:00:02 PST
