Re: [AMBER] Regarding antechamber command Error

From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
Date: Thu, 11 Aug 2016 18:37:53 +0530

Dear Sir,

all necessary hydrogens are present in lig.pdb. I have checked the file and
then execute the antechamber command. The log.pdb file is also attached
herewith plz check the same.

Thanks in advance..

On Thu, Aug 11, 2016 at 5:22 PM, David A Case <david.case.rutgers.edu>
wrote:

> 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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>



-- 
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 Thu Aug 11 2016 - 06:30:02 PDT
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