On Wed, Aug 10, 2016, Vishal Nemaysh wrote:
>
> 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.
>
> *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*
Something is wrong with the coordinates in the "lig.pdb" file: have you
visualized this structure? Are all the hydrogen atoms present?
> *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*
The error message will be in the sqm.out file.
...dac
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Received on Thu Aug 11 2016 - 05:00:02 PDT
