[gmx-users] Selection Error for RDF calculations
Pandya, Akash
akash.pandya.15 at ucl.ac.uk
Tue Dec 12 23:12:42 CET 2017
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?
Akash
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