[gmx-users] Index error

[Justin Lemkul]

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
20 Penn St.
Baltimore, MD 21201

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

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