[gmx-users] Index error

Justin Lemkul jalemkul at vt.edu
Wed Jul 24 14:36:45 CEST 2013



On 7/24/13 8:34 AM, Collins Nganou wrote:
> Dear Users,
>
> I would like to know if anyone may help me understand how to update the
> index file.
> I am trying to simulate a dna in solution.
> I have relaxed a Solvent with attached min.mdp file without problem. in
> the second step I was intended to relax SOL + Na  DNA with 20ps.mdp. But
> the index file did not work.
> I have trying to generate an index file using the file.gro from min.mdp but
> it doesn't work.
>

It is simple to merge solvent and ion groups.  See tutorial material or type 
'help' at the make_ndx prompt.  We can't help you if we don't know what you did.

> Below is the obtained error.
>
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning H bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning H bonds into constraints...
> Velocities were taken from a Maxwell distribution at 10 K
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line:
> 1332
>
> Fatal error:
> Group NA+SOL referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>

If you use make_ndx, group names will never contain + signs.  Merged groups are 
joined via _ (underscore), but it sounds like you haven't even gotten that far, 
given the statement above.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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