[AMBER] Regarding antechamber command Error

From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
Date: Wed, 10 Aug 2016 21:17:05 +0530

Hello Sir,

I have face the error when i used the command "*antechamber -i lig.pdb -fi
pdb -o lig.mol2 -fo mol2 -c bcc -s 2*" in antechamber, which can showed the
following massege.
Plz suggest me how can i resolve this problem.

*[vnemaysh.localhost T2A_Complex]$ antechamber -i lig.pdb -fi pdb -o
lig.mol2 -fo mol2 -c bcc -s 2*

*Running: /home/vnemaysh/Desktop/Amber_12/amber12/bin/bondtype -j full -i

*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*

*Running: /home/vnemaysh/Desktop/Amber_12/amber12/bin/atomtype -i

*Total number of electrons: 188; net charge: 0*

*Running: /home/vnemaysh/Desktop/Amber_12/amber12/bin/sqm -O -i sqm.in
<http://sqm.in> -o sqm.out*

*Error: cannot run "/home/vnemaysh/Desktop/Amber_12/amber12/bin/sqm -O -i
sqm.in <http://sqm.in> -o sqm.out" of bcc() in charge.c properly, exit*

Thanking You,
Vishal Nemaysh
Research Scholar,
Neuropharmaceutical Chemistry Group,
Dr. B. R. Ambedkar Center for Biomedical Research,
University of Delhi, Delhi-110007
Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
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Received on Wed Aug 10 2016 - 09:00:03 PDT
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