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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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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 - 11:00:09 PDT
