[gmx-users] Urea topology problem

Fri Dec 19 12:37:50 CET 2008

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?
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> 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> > > >> > > >> > > > > > ------------------------------------------------------------------------> > > > ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo > > gratis> > > > <http://vivelive.com/ieak7/>> > > >> > > >> > > > > > ------------------------------------------------------------------------> > > >> > > > _______________________________________________> > > > gmx-users mailing list gmx-users at gromacs.org> > > > http://www.gromacs.org/mailman/listinfo/gmx-users> > > > Please search the archive at http://www.gromacs.org/search before > > posting!> > > > Please don't post (un)subscribe requests to the list. Use the> > > > www interface or send it to gmx-users-request at gromacs.org.> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> > >> > > --> > > ========================================> > >> > > 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> > >> > > ========================================> > > _______________________________________________> > > gmx-users mailing list gmx-users at gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/search before > > posting!> > > Please don't post (un)subscribe requests to the list. Use the> > > www interface or send it to gmx-users-request at gromacs.org.> > > Can't post? 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Fax: +4618511755.> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se> _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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