[gmx-users] Urea topology problem

[Justin A. Lemkul]

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
>  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
>  > >
>  > >
>  > > 
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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
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

========================================