Distance between ion and coordinating residue

User discussions
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GROMACS version: 2021.3
GROMACS modification: No

Hi all users!,

I am trying to use the distance function within Gromacs to measure the average distance between a Zinc ion and a coordinating residue e.g, Histidine (NE2) or cysteine (SG). I have created index file with specific groups for the coordinating residues and the zinc ion but the error message I get is that the selection does not equal into an even number of positions.

How do i solve/overcome this issue?
Can I use the -select option if so how does the syntax for this work?

Any help would be greatly appreciated! :)

With regards,
Dan.

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For those who may have a similar problem, my steps to solve this problem was:

  1. Create an index file with the atoms you want to calculate the distance between e.g.
    r “X” & a “atom selection” where X = residue number and atom selection is the atom you which to select e.g., SG, NE2, OD1 etc.

  2. Then merge the two groups together, so if your selection was 1 and 2 then type 1 | 2 to merge the groups.

Hope this helps!

Dan.

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You can also see examples and lots of helpful documentation with gmx help selections (subtopics cmdline and examples are particularly useful).