Hi,
I can confirm that this bug exists, but I'm not sure whats causing it.
That said, I'm not sure how well prepgen is maintained or supported
anymore. Could you maybe put receptor_resp_gaff.ac into a different
format (like mol2) and use antechamber to generate your prep file?
-Dan
On Thu, May 7, 2015 at 9:12 AM, Rebeca García Fandiño
<regafan.hotmail.com> wrote:
> 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
>> >
>> >
>> > _______________________________________________
>> > 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 07 2015 - 10:00:02 PDT
