Hi,
If you are trying to prepare a protein for simulation this is *not*
the way. Antechamber should really only be used for parameterizing
small molecules only. You probably just want to use leap to create a
topology file and initial coordinates. If you haven't already, the
Amber basic tutorials are a good place to start to become familiar
with how simulations with Amber work: http://ambermd.org/tutorials/
Hope this helps,
-Dan
On Thu, Sep 18, 2014 at 8:37 AM, Vishal Nemaysh
<vishal.bioinfotech.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Sep 18 2014 - 08:00:05 PDT
