Hi sir,
i want to prepare the initial topology file for my protein of interest..for
this i use the command make the mol2 format file ...
antechamber -i 1YCC_h.pdb -fi pdb -o 1YCC_h.mol2 -fo mol2 -c bcc -s 2
but the error is appear as i mention i my last mail .....sir as u suggest
about the sqm.out file ....
in sqm.out only few lines are appear whih are as follow...
QMMM: System specified with odd number of electrons ( 2825)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
calculation.
i have try to find the solution in google ...but there is no any solution
found...
sir plz suggest me how to overcome this problume
On Thu, Sep 18, 2014 at 5:27 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, 2014-09-18 at 15:20 +0530, Vishal Nemaysh wrote:
> > Hi all,
> >
> > I am a newbie to use the AMBER 12. i have encountered the following
> problem
> > during .pdb file to mol2 file convertion. my pdb file is attached
> herewith.
> >
> >
> > *Running: /home/vnemaysh/Desktop/AMBER12/amber12/bin/sqm -O -i sqm.in
> > <http://sqm.in> -o sqm.outError: cannot run
> > "/home/vnemaysh/Desktop/AMBER12/amber12/bin/sqm -O -i sqm.in
> > <http://sqm.in> -o sqm.out" of bcc() in charge.c properly, exit*
>
> Have a look in the sqm.out file for an error message. Then google the
> error message itself to see if your problem has been reported and
> answered before (it most likely has).
>
> If you are still stuck, reply back here with a more detailed description
> of what you did and what went wrong (and by detailed description I mean
> tell us the exact commands you used and the exact error messages you
> received with the relevant context).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vishal
Research Scholar,
Neuropharmaceutical Chemistry lab.,
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+9650736653
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Received on Thu Sep 18 2014 - 08:00:03 PDT
