[gmx-users] Urea topology problem
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 19 13:33:07 CET 2008
Rebeca García Fandiño wrote:
> OK, including a mass colum, as Justin A. Lemkul suggested, worked well.
> Now grompp does not give errors.
> Why should I not use this model for urea? I have found also another
> model in the contributions section, for a urea/water box 10M, but why
> should I trust more in a user contribution than in a *itp included in
> Gromacs?
It is your responsibility to choose the right force field for the job,
hence you have to read the literature.
Maybe we should remove those itp file that are not coupled to a
published force field.
> I don´t have much experience with Gromacs, so any coment will be wellcome.
> Thank you very much for your help and suggestions.
> Best wishes,
>
> Rebeca García
> Parc Cientific de Barcelona
> regafan at hotmail.com <mailto:regafan at hotmail.com>
>
> > Date: Thu, 18 Dec 2008 19:50:03 +0100
> > From: spoel at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Urea topology problem
> >
> > Rebeca García Fandiño wrote:
> > > Hello,
> > > I don´t understand the correction I should do from itp.
> > > I have removed from the urea original urea.itp these lines,
> >
> > don't use this model. do a proper literature search.
> >
> > >
> > > #ifdef Boek
> > > 1 C 1 UREA C1 1 0.38
> > > 2 O 1 UREA O2 1 -0.38
> > > 3 NT 1 UREA N3 2 -0.83
> > > 4 H 1 UREA H4 2 0.415
> > > 5 H 1 UREA H5 2 0.415
> > > 6 NT 1 UREA N6 3 -0.83
> > > 7 H 1 UREA H7 3 0.415
> > > 8 H 1 UREA H8 3 0.415
> > > #else
> > > #endif[ moleculetype ]
> > >
> > > so now, my urea.itp file is:
> > >
> > > ; name nrexcl
> > > Urea 3
> > > [ atoms ]
> > > ; nr type resnr residu atom cgnr charge
> > > 1 C 1 UREA C1 1 0.683
> > > 2 O 1 UREA O2 1 -0.683
> > > 3 NT 1 UREA N3 2 -0.622
> > > 4 H 1 UREA H4 2 0.346
> > > 5 H 1 UREA H5 2 0.276
> > > 6 NT 1 UREA N6 3 -0.622
> > > 7 H 1 UREA H7 3 0.346
> > > 8 H 1 UREA H8 3 0.276
> > > [ bonds ]
> > > ; ai aj funct b0 kb
> > > 3 4 1 1.000000e-01 3.744680e+05
> > > 3 5 1 1.000000e-01 3.744680e+05
> > > 6 7 1 1.000000e-01 3.744680e+05
> > > 6 8 1 1.000000e-01 3.744680e+05
> > > 1 2 1 1.230000e-01 5.020800e+05
> > > 1 3 1 1.330000e-01 3.765600e+05
> > > 1 6 1 1.330000e-01 3.765600e+05
> > > [ pairs ]
> > > ; ai aj funct c6 c12
> > > 2 4 1 0.000000e+00 0.000000e+00
> > > 2 5 1 0.000000e+00 0.000000e+00
> > > 2 7 1 0.000000e+00 0.000000e+00
> > > 2 8 1 0.000000e+00 0.000000e+00
> > > 3 7 1 0.000000e+00 0.000000e+00
> > > 3 8 1 0.000000e+00 0.000000e+00
> > > 4 6 1 0.000000e+00 0.000000e+00
> > > 5 6 1 0.000000e+00 0.000000e+00
> > > [ angles ]
> > > ; ai aj ak funct th0 cth
> > > 1 3 4 1 1.200000e+02 2.928800e+02
> > > 1 3 5 1 1.200000e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02
> > > 3 1 6 1 1.170000e+02 5.020800e+02
> > > [ dihedrals ]
> > > ; ai aj ak al funct phi cp mult
> > > 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 6 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 2 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 6 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 2 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 3 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 2 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > 3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
> > > [ dihedrals ]
> > > ; ai aj ak al funct q0 cq
> > > 3 4 5 1 2 0.000000e+00 1.673600e+02
> > > 6 7 8 1 2 0.000000e+00 1.673600e+02
> > > 1 3 6 2 2 0.000000e+00 1.673600e+02
> > >
> > > 4 3 5 1 1.200000e+02 3.347200e+02
> > > 1 6 7 1 1.200000e+02 2.928800e+02
> > > 1 6 8 1 1.200000e+02 2.928800e+02
> > > 7 6 8 1 1.200000e+02 3.347200e+02
> > > 2 1 3 1 1.215000e+02 5.020800e+02
> > >
> > >
> > > Following Chapter 5 in the manual (page 102), the file described for
> > > urea.itp is the same as mine. For the topology (page 103)
> > > #include "ffgmx.itp" is used, but I don´t see any more different.
> > > With this modification in the urea.itp I get the same error. Any
> idea of
> > > what could be the problem?
> > > Thank you very much for your help,
> > >
> > > Rebeca Garcia
> > > Parc Cientific de Barcelona
> > > regafan at hotmail.com <mailto:regafan at hotmail.com>
> > >
> > >
> > >
> > >
> > >
> > > > Date: Thu, 18 Dec 2008 09:21:41 -0500
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] Urea topology problem
> > > >
> > > >
> > > >
> > > > Rebeca García Fandiño wrote:
> > > >
> > > > <snip>
> > > >
> > > > >
> > > > > ERROR 1 [file solvated.top, line 39]:
> > > > >
> > > > > atom C1 (Res UREA-1) has mass 0
> > > > >
> > > > >
> > > >
> > > > In urea.itp, no masses are defined. If you correct the format of
> this
> > > file (see
> > > > Chapter 5 of the manual), then this issue should be resolved.
> > > >
> > > >
> > > > >
> > > > > Which force field does this urea.itp correspond to? Where
> should it
> > > look
> > > > > for the atomtypes of urea?
> > > > >
> > > > >
> > > >
> > > > The .atp file corresponding to the force field you are using
> > > (ffG43a2). The
> > > > atomtypes for urea appear to be generic for use with the Gromos96
> > > force fields.
> > > > There are specific atomtypes within ffG53a6 for urea, if you want to
> > > use the
> > > > newer force field (check the ffG53a6.rtp file for the urea
> parameters).
> > > >
> > > > -Justin
> > > >
> > > >
> > > > >
> > > > > Thank you very much for your help,
> > > > >
> > > > >
> > > > >
> > > > > Rebeca Garcia
> > > > >
> > > > > Parc Cientific de Barcelona
> > > > >
> > > > > regafan at hotmail.com
> > > > >
> > > > >
> > > > >
> > >
> ------------------------------------------------------------------------
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> > > > >
> > >
> ------------------------------------------------------------------------
> > > > >
> > > > > _______________________________________________
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> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Graduate Research Assistant
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
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> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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