Thanks a lot, Daniel.
Now it works :-)
> Date: Thu, 7 May 2015 11:54:20 -0600
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] problem with prepgen in an organic molecule parameterization
>
> On Thu, May 7, 2015 at 11:05 AM, Rebeca García Fandiño
> <regafan.hotmail.com> wrote:
> > What I am doing at the moment is:
> >
> > $AMBERHOME/bin/antechamber -i receptor_min.pdb -fi pdb -o receptor.mol2 -fo mol2 -c gas -s 2 -nc 0
>
> Why not from this point just use parmchk and the mol2 file in tleap?
>
> parmchk -i receptor.mol2 -f mol2 -o receptor.frcmod
>
> Then in tleap:
>
> source leaprc.gaff
> loadamberparams receptor.frcmod
> MOL = loadmol2 receptor.mol2
>
> and so on.
>
> Also, be cautious - in my opinion the charge scheme you are using
> (Gasteiger) isn't really optimal. Ideally you would use RESP-fitting
> of ESP obtained at HF/6-31G* level, especially if you're also using
> one of the Amber protein force fields (which it seems like you are).
> They may be a good rough estimate, but I would do some careful
> validation and probably wouldn't use them for anything sensitive.
> There are some tools out there that can automate this procedure you
> may want to look into (e.g. R.E.D. server).
>
> Hope this helps,
>
> -Dan
>
> > $AMBERHOME/bin/antechamber -i receptor.mol2 -fi mol2 -o receptor.ac -fo ac -nc 0
> > $AMBERHOME/bin/atomtype -i receptor.ac -o receptor_resp_gaff.ac -p gaff
> > $AMBERHOME/bin/prepgen -i receptor_resp_gaff.ac -o receptor_resp_gaff.prepc -f car
> > $AMBERHOME/bin/parmchk -i receptor_resp_gaff.prepc -o receptor.frcmod -f prepc
> >
> > And then, in Leap:
> >
> > source leaprc.ff99SB
> > loadamberparams ./gaff.dat
> > loadamberparams receptor.frcmod
> > loadamberprep receptor_resp_gaff.prepc
> > saveoff MOL monomero.lib
> > saveamberparm MOL receptor.top receptor.crd
> > quit
> >
> > Which would be the alternative without using prepgen?
> >
> > Rebeca
> >
> >
> >> Date: Thu, 7 May 2015 10:31:01 -0600
> >> From: daniel.r.roe.gmail.com
> >> To: amber.ambermd.org
> >> Subject: Re: [AMBER] problem with prepgen in an organic molecule parameterization
> >>
> >> 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)
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
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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 Fri May 08 2015 - 02:30:03 PDT
