I am using Ambertools 14, and the file receptor_resp_gaff.ac is attached.
Thanks a lot for your help!
Rebeca
> Date: Thu, 7 May 2015 08:51:09 -0600
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] problem with prepgen in an organic molecule parameterization
>
> Hi,
>
> I think we need a bit more information to go on. What version of
> AmberTools are you using? Can you attach the file
> "receptor_resp_gaff.ac" (if it is small enough) so we can try to
> reproduce the error? Thanks,
>
> -Dan
>
>
> On Thu, May 7, 2015 at 8:37 AM, Rebeca García Fandiño
> <regafan.hotmail.com> wrote:
> > Dear Amber users,
> > I am trying to parameterize an organic molecule (109 atoms), and in the step
> >
> > $AMBERHOME/bin/prepgen -i receptor_resp_gaff.ac -o receptor_resp_gaff.prepc -f car
> >
> > I obtain an incorrect prepc file, where all the atoms after 37 have lines filled from zeros.
> >
> > 0 0 2
> >
> > This is a remark line
> > molecule.res
> > MOL XYZ 0
> > CHANGE OMIT DU BEG
> > 0.0000
> > 1 DUMM DU M 999.000 999.0 -999.0 .00000
> > 2 DUMM DU M 999.000 -999.0 999.0 .00000
> > 3 DUMM DU M -999.000 999.0 999.0 .00000
> > 4 C13 c2 M -1.463000 4.538000 2.303000 -0.117501
> > (...)
> > 36 H18 hc E -9.404000 3.700000 4.423000 0.023308
> > 37 H19 hc E -10.004000 5.386000 4.547000 0.023308
> > 38 X 0.000000 0.000000 0.000000 0.000000
> > 39 X 0.000000 0.000000 0.000000 0.000000
> > 40 X 0.000000 0.000000 0.000000 0.000000
> > 41 X 0.000000 0.000000 0.000000 0.000000
> > 42 X 0.000000 0.000000 0.000000 0.000000
> > (...)
> >
> > In the file "receptor_resp_gaff.ac" all these lines are correctly completed.
> >
> > Any idea of why is this happening?
> >
> > Best wishes,
> >
> > Rebeca.
> >
> > Dr. Rebeca Garcia
> > Santiago de Compostela University
> > Spain
> >
> >
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> > 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 May 07 2015 - 08:30:02 PDT
