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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--
-------------------------
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 - 08:00:04 PDT
