[gmx-users] Urea topology problem
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 18 19:50:03 CET 2008
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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