[gmx-users] Selection Error for RDF calculations
jalemkul at vt.edu
Tue Dec 12 23:21:59 CET 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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