[gmx-users] Grompp error on index file

[Justin A. Lemkul]

Mr Bernard Ramos wrote:
> Hi Justin,
>  
> Thanks for the immediate response. I apologize but I don't have with me 
> the mdp and the top files at the moment. But I will have it e-mailed 
> once I get back to my working gromacs computer.
>  
> Yes, as I remember, the [moleculetype] at the bottom of the topol.top 
> was able to identify it as a carbohydrate. In fact, the index.file 
> identified it as a carbohydrate. I borrowed the nvt.mdp from the 
> Lysozyme tutorial authored by you. Thanks.
> 

Then that may be your problem.  What's in your system?  Do you have any protein? 
  If you don't, then you can't specify "protein" in the .mdp file.  The problem 
is not the index file, it's the .mdp file.  In some cases, the error message 
gives you the wrong impression; it really means that a group in the .mdp file 
does not exist.  In most cases, that means you need to create an index group to 
accommodate the system.  In other cases, it means you're using a group that is 
simply not applicable.

-Justin

> 
> --- On *Tue, 5/31/11, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] Grompp error on index file
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Tuesday, May 31, 2011, 10:09 AM
> 
> 
> 
>     Mr Bernard Ramos wrote:
>      > Hi everyone!
>      >  I added a residue on the gromacs 4.5.3 I have. I followed the
>     instructions as indicated in the "Adding A Residue to a Force Field"
>     with this link
>     _http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_.
>     I added the residue to residuetypes.dat and indicated it as a
>     carbohydrate. The topology in fact was able to write it down as a
>     carbohydrate.
>      > 
> 
>     Carbohydrates should be grouped into the "other" category; I'm not
>     sure "Carbohydrate" is a recognized type.  What do you mean the
>     topology wrote it as a carbohydrate?  Is that the [moleculetype]
>     name it was given the topology?
> 
>      > __
>      > Generating a topology went well with pdb2gmx, editconf, genbox,
>     energy minimization. However, I encountered the following error when
>     I was about to do an NVT equilibration.
>      > 
>     ----------------------------------------------------------------------------------------------------------------------------------
>      > Program grompp, VERSION 4.5.3
>      > Source code file: readir.c, line: 1316
>      > Fatal error:
>      > Group protein not found in indexfile.
>      > Maybe you have non-default groups in your mdp file, while not
>     using the '-n' option of grompp.
>      > In that case use the '-n'option.
>      >
>     ----------------------------------------------------------------------------------------------------------------------------------
>      >  In response, I created an index file using make_ndx. The index
>     file was able to generate correctly the molecule indices and
>     identified it correctly as indicated in the residuetypes.dat and
>     carbohydrate.rtp
>      > 
> 
>     Your error does not appear to be connected to the carbohydrate at
>     all.  The problem appears to be the use of "protein." 
>     Capitalization shouldn't matter, so I'm not sure why grompp is
>     complaining.
> 
>      > And then I tried (again) the following command:
>      >  $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o
>     nvt.tpr.
>      >  It still generates the same error as above. Please help
>      >
> 
>     Please provide your .mdp file and topology, if it is small enough to
>     paste into an email.
> 
>     -Justin
> 
>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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