[gmx-users] Urea topology problem

Thu Dec 18 19:42:00 CET 2008

Hello,
I don´t understand the correction I should do from itp. 
I have removed from the urea original urea.itp these lines,

#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 nrexclUrea 3
[ atoms ]; nr type resnr residu atom cgnr charge1 C 1 UREA C1 1 0.6832 O 1 UREA O2 1 -0.6833 NT 1 UREA N3 2 -0.6224 H 1 UREA H4 2 0.3465 H 1 UREA H5 2 0.2766 NT 1 UREA N6 3 -0.6227 H 1 UREA H7 3 0.3468 H 1 UREA H8 3 0.276
[ bonds ]; ai aj funct b0 kb3 4 1 1.000000e-01 3.744680e+053 5 1 1.000000e-01 3.744680e+056 7 1 1.000000e-01 3.744680e+056 8 1 1.000000e-01 3.744680e+051 2 1 1.230000e-01 5.020800e+051 3 1 1.330000e-01 3.765600e+051 6 1 1.330000e-01 3.765600e+05
[ pairs ]; ai aj funct c6 c122 4 1 0.000000e+00 0.000000e+002 5 1 0.000000e+00 0.000000e+002 7 1 0.000000e+00 0.000000e+002 8 1 0.000000e+00 0.000000e+003 7 1 0.000000e+00 0.000000e+003 8 1 0.000000e+00 0.000000e+004 6 1 0.000000e+00 0.000000e+005 6 1 0.000000e+00 0.000000e+00
[ angles ]; ai aj ak funct th0 cth1 3 4 1 1.200000e+02 2.928800e+021 3 5 1 1.200000e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+023 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+006 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+002 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+006 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+002 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+003 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+002 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+003 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
[ dihedrals ]; ai aj ak al funct q0 cq3 4 5 1 2 0.000000e+00 1.673600e+026 7 8 1 2 0.000000e+00 1.673600e+021 3 6 2 2 0.000000e+00 1.673600e+024 3 5 1 1.200000e+02 3.347200e+021 6 7 1 1.200000e+02 2.928800e+021 6 8 1 1.200000e+02 2.928800e+027 6 8 1 1.200000e+02 3.347200e+022 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

> 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? Read http://www.gromacs.org/mailing_lists/users.php
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