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 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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> ========================================> > 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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