[gmx-users] Grompp error on index file

Mr Bernard Ramos bgrquantum at yahoo.com
Tue May 31 04:23:12 CEST 2011

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. 

--- 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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