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
rega...@hotmail.com <mailto:rega...@hotmail.com>
> Date: Thu, 18 Dec 2008 19:50:03 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@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
> > rega...@hotmail.com <mailto:rega...@hotmail.com>
> >
> >
> >
> >
> >
> > > Date: Thu, 18 Dec 2008 09:21:41 -0500
> > > From: jalem...@vt.edu
> > > To: gmx-users@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
> > > >
> > > > rega...@hotmail.com
> > > >
> > > >
> > > >
> >
------------------------------------------------------------------------
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> > > >
> > > >
> > > >
> >
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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.
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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