[AMBER] error for antecamber to establish small molecule

From: Zhou Gong <zgong.hust.gmail.com>
Date: Wed, 8 Dec 2010 22:58:49 +0800

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
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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Received on Wed Dec 08 2010 - 07:00:02 PST
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