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
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC
<
http://ANTECHAMBER_BOND_TYPE.AC> -f ac*
*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
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC <
http://ANTECHAMBER_AC.AC> -p gaff*
*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
