[gmx-users] grompp errors..

[Justin Lemkul]

On 9/29/12 12:55 PM, Ali Alizadeh wrote:
> Dear All users
>
> I have a system with 3 layers,
> when i run grompp program, encounter with this error.
> First and 3th layer is the same, and middle layer is water. what's
> this error about?

grompp is looking for some group called "1" (the number one) but it can't find 
such a group.  The error suggests that you use a custom index group.  In the 
absence of an .mdp file and a list of the index groups that you're trying to 
use, we can't really guess what's supposed to be happening.

> and i have another question about make_ndx, How to make index the same
> atoms with different res number  in .gro file?
>

Type "help" at the make_ndx prompt to see examples.  If you need specific help 
with a specific task, ask a more specific question :)

-Justin

> ..........................................
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Ignoring obsolete mdp entry 'nstcheckpoint'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Ion'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Ion2'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Analysing residue names:
> There are:  1183        Ion residues
> There are:  1830      Water residues
> Analysing residues not classified as Protein/DNA/RNA/Water and
> splitting into groups...
> Number of degrees of freedom in T-Coupling group System is 23990.00
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1320
>
> Fatal error:
> Group 1 not found in 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.
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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