[gmx-users] Selection Error for RDF calculations

[Justin Lemkul]

On 12/12/17 5:12 PM, Pandya, Akash wrote:
> Hi all,
>
> I am trying to calculate the RDF in system with my protein and also glycine. I have made a custom index groups for the protein and also the glycine as show below:
>
>
>> ri 1-442
> Found 6615 atoms with resind.+1 in range 1-442
>
> 24 r_1-442             :  6615 atoms
>
>> ri 466-619
> Found 1540 atoms with resind.+1 in range 466-619
>
> 25 r_466-619           :  1540 atoms
>
>
> When I type in the appropriate command:
>
> gmx rdf -f protein_gly.gro -n protein_gly.ndx -b 0 -e 60000 -tu ns -o rdf.xvg -norm rdf -bin 0.2
>
>
>
> I get the following error when I finish selecting the 'ref' which is the protein and `sel` which is the glycine molecules
>
>
> Inconsistency in user input:
> Invalid index group references encountered
>    Group 'r_466-619' cannot be used in selections, because it contains negative
>    atom indices and/or references atoms not present (largest allowed atom index
>    is 8155).
>
> Please can someone advise me on what I should do?

Does protein_gly.gro contain the whole system, or did you do something 
like remove water? You need to create an index file using a matching 
reference, and the most common issue is not saving water but creating an 
index group based on a full system. Hence the indices would be out of range.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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