Re: [AMBER] Regarding antechamber command Error

From: David A Case <>
Date: Thu, 11 Aug 2016 07:52:43 -0400

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
> <> -o sqm.out" of bcc() in charge.c properly, exit*

The error message will be in the sqm.out file.


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Received on Thu Aug 11 2016 - 05:00:02 PDT
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