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OK, including a mass colum, as Justin A. Lemkul suggested, worked well. Now grompp does not give errors.<BR>
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?<BR>
I don´t have much experience with Gromacs, so any coment will be wellcome. <BR>
Thank you very much for your help and suggestions.<BR>
Best wishes,<BR>
<BR>
Rebeca García <BR>
Parc Cientific de Barcelona<BR>
<A href="mailto:regafan@hotmail.com">regafan@hotmail.com</A><BR><BR>> Date: Thu, 18 Dec 2008 19:50:03 +0100<BR>> From: spoel@xray.bmc.uu.se<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] Urea topology problem<BR>> <BR>> Rebeca García Fandiño wrote:<BR>> > Hello,<BR>> > I don´t understand the correction I should do from itp.<BR>> > I have removed from the urea original urea.itp these lines,<BR>> <BR>> don't use this model. do a proper literature search.<BR>> <BR>> > <BR>> > #ifdef Boek<BR>> > 1 C 1 UREA C1 1 0.38<BR>> > 2 O 1 UREA O2 1 -0.38<BR>> > 3 NT 1 UREA N3 2 -0.83<BR>> > 4 H 1 UREA H4 2 0.415<BR>> > 5 H 1 UREA H5 2 0.415<BR>> > 6 NT 1 UREA N6 3 -0.83<BR>> > 7 H 1 UREA H7 3 0.415<BR>> > 8 H 1 UREA H8 3 0.415<BR>> > #else<BR>> > #endif[ moleculetype ]<BR>> > <BR>> > so now, my urea.itp file is:<BR>> > <BR>> > ; name nrexcl<BR>> > Urea 3<BR>> > [ atoms ]<BR>> > ; nr type resnr residu atom cgnr charge<BR>> > 1 C 1 UREA C1 1 0.683<BR>> > 2 O 1 UREA O2 1 -0.683<BR>> > 3 NT 1 UREA N3 2 -0.622<BR>> > 4 H 1 UREA H4 2 0.346<BR>> > 5 H 1 UREA H5 2 0.276<BR>> > 6 NT 1 UREA N6 3 -0.622<BR>> > 7 H 1 UREA H7 3 0.346<BR>> > 8 H 1 UREA H8 3 0.276<BR>> > [ bonds ]<BR>> > ; ai aj funct b0 kb<BR>> > 3 4 1 1.000000e-01 3.744680e+05<BR>> > 3 5 1 1.000000e-01 3.744680e+05<BR>> > 6 7 1 1.000000e-01 3.744680e+05<BR>> > 6 8 1 1.000000e-01 3.744680e+05<BR>> > 1 2 1 1.230000e-01 5.020800e+05<BR>> > 1 3 1 1.330000e-01 3.765600e+05<BR>> > 1 6 1 1.330000e-01 3.765600e+05<BR>> > [ pairs ]<BR>> > ; ai aj funct c6 c12<BR>> > 2 4 1 0.000000e+00 0.000000e+00<BR>> > 2 5 1 0.000000e+00 0.000000e+00<BR>> > 2 7 1 0.000000e+00 0.000000e+00<BR>> > 2 8 1 0.000000e+00 0.000000e+00<BR>> > 3 7 1 0.000000e+00 0.000000e+00<BR>> > 3 8 1 0.000000e+00 0.000000e+00<BR>> > 4 6 1 0.000000e+00 0.000000e+00<BR>> > 5 6 1 0.000000e+00 0.000000e+00<BR>> > [ angles ]<BR>> > ; ai aj ak funct th0 cth<BR>> > 1 3 4 1 1.200000e+02 2.928800e+02<BR>> > 1 3 5 1 1.200000e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02<BR>> > 3 1 6 1 1.170000e+02 5.020800e+02<BR>> > [ dihedrals ]<BR>> > ; ai aj ak al funct phi cp mult<BR>> > 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 6 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 2 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 6 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 2 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 3 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 2 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > 3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00<BR>> > [ dihedrals ]<BR>> > ; ai aj ak al funct q0 cq<BR>> > 3 4 5 1 2 0.000000e+00 1.673600e+02<BR>> > 6 7 8 1 2 0.000000e+00 1.673600e+02<BR>> > 1 3 6 2 2 0.000000e+00 1.673600e+02<BR>> > <BR>> > 4 3 5 1 1.200000e+02 3.347200e+02<BR>> > 1 6 7 1 1.200000e+02 2.928800e+02<BR>> > 1 6 8 1 1.200000e+02 2.928800e+02<BR>> > 7 6 8 1 1.200000e+02 3.347200e+02<BR>> > 2 1 3 1 1.215000e+02 5.020800e+02<BR>> > <BR>> > <BR>> > Following Chapter 5 in the manual (page 102), the file described for <BR>> > urea.itp is the same as mine. For the topology (page 103)<BR>> > #include "ffgmx.itp" is used, but I don´t see any more different.<BR>> > With this modification in the urea.itp I get the same error. Any idea of <BR>> > what could be the problem?<BR>> > Thank you very much for your help,<BR>> > <BR>> > Rebeca Garcia <BR>> > Parc Cientific de Barcelona<BR>> > regafan@hotmail.com <mailto:regafan@hotmail.com><BR>> > <BR>> > <BR>> > <BR>> > <BR>> > <BR>> > > Date: Thu, 18 Dec 2008 09:21:41 -0500<BR>> > > From: jalemkul@vt.edu<BR>> > > To: gmx-users@gromacs.org<BR>> > > Subject: Re: [gmx-users] Urea topology problem<BR>> > ><BR>> > ><BR>> > ><BR>> > > Rebeca García Fandiño wrote:<BR>> > ><BR>> > > <snip><BR>> > ><BR>> > > ><BR>> > > > ERROR 1 [file solvated.top, line 39]:<BR>> > > ><BR>> > > > atom C1 (Res UREA-1) has mass 0<BR>> > > ><BR>> > > ><BR>> > ><BR>> > > In urea.itp, no masses are defined. If you correct the format of this <BR>> > file (see<BR>> > > Chapter 5 of the manual), then this issue should be resolved.<BR>> > ><BR>> > ><BR>> > > ><BR>> > > > Which force field does this urea.itp correspond to? Where should it <BR>> > look<BR>> > > > for the atomtypes of urea?<BR>> > > ><BR>> > > ><BR>> > ><BR>> > > The .atp file corresponding to the force field you are using <BR>> > (ffG43a2). The<BR>> > > atomtypes for urea appear to be generic for use with the Gromos96 <BR>> > force fields.<BR>> > > There are specific atomtypes within ffG53a6 for urea, if you want to <BR>> > use the<BR>> > > newer force field (check the ffG53a6.rtp file for the urea parameters).<BR>> > ><BR>> > > -Justin<BR>> > ><BR>> > ><BR>> > > ><BR>> > > > Thank you very much for your help,<BR>> > > ><BR>> > > ><BR>> > > ><BR>> > > > Rebeca Garcia<BR>> > > ><BR>> > > > Parc Cientific de Barcelona<BR>> > > ><BR>> > > > regafan@hotmail.com<BR>> > > ><BR>> > > ><BR>> > > > <BR>> > ------------------------------------------------------------------------<BR>> > > > ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo <BR>> > gratis<BR>> > > > <http://vivelive.com/ieak7/><BR>> > > ><BR>> > > ><BR>> > > > <BR>> > ------------------------------------------------------------------------<BR>> > > ><BR>> > > > _______________________________________________<BR>> > > > gmx-users mailing list gmx-users@gromacs.org<BR>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > > > Please search the archive at http://www.gromacs.org/search before <BR>> > posting!<BR>> > > > Please don't post (un)subscribe requests to the list. Use the<BR>> > > > www interface or send it to gmx-users-request@gromacs.org.<BR>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> > ><BR>> > > --<BR>> > > ========================================<BR>> > ><BR>> > > Justin A. Lemkul<BR>> > > Graduate Research Assistant<BR>> > > Department of Biochemistry<BR>> > > Virginia Tech<BR>> > > Blacksburg, VA<BR>> > > jalemkul[at]vt.edu | (540) 231-9080<BR>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> > ><BR>> > > ========================================<BR>> > > _______________________________________________<BR>> > > gmx-users mailing list gmx-users@gromacs.org<BR>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > > Please search the archive at http://www.gromacs.org/search before <BR>> > posting!<BR>> > > Please don't post (un)subscribe requests to the list. Use the<BR>> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> > > Can't post? 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