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,
The error message was that grompp couldn't find masses for these atoms. The
correct format should include a mass column after the charge column (see, for
example, your protein topology from pdb2gmx). I guess the manual needs a bit of
revision.
<snip>
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?
As a general warning, don't use ffgmx. It is deprecated. Stick with Gromos96,
as you had initially intended.
-Justin
Thank you very much for your help,
Rebeca Garcia
Parc Cientific de Barcelona
rega...@hotmail.com <mailto: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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> >
> >
> >
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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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========================================
Justin A. Lemkul
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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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