Creating a group for RMSD analysis

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1

GROMACS version:
GROMACS modification: Yes/No
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GROMACS: gmx rms, version 2020.1-Ubuntu-2020.1-1

I am doing the RMSD analysis of a protein, and would like to include specific domains such as a number of residues for beta sheet/strands, alpha helix, pore region, etc. How would I go about that to create a special group with these specific domains using the residue numbers? Is this possible?

Thank you,
Heather

2

Via make_ndx, you can select stretches of residues, i.e.

r 1-50 | r 76-90 | r 101-125
3

ok, so just to clarify for command. I could do:

gmx make_ndx -f md_0_1.gro r 1-50 | r 76-90 | r 101-125 -o index.ndx

gmx rms -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o residues.xvg

?? I am still learning, thanks in advance.

4

or do I do:

gmx make_ndx -f md_0_1.gro -o index.ndx

default selection screen appears…then I enter r 1-50 | r 76-90 | r 101-125 ??

and then continue with the gmx rms?

5

Yes, this is the correct approach. make_ndx is an interactive program. Supply whatever residue numbers you need. Type help at the prompt to see example syntax.

6

A follow up query, If there are more than 1 chain in the system, how to select residues for the indexing purpose?
for say, I want to make index of ChainA, ChainB and ChainC for residues 1-10, 100-110 and 85-95 respectively. What should be the input for the gmx make_ndx -f MD.gro -o index.ndx?

Thanks

7

You can select by chain if you supply a PDB file that contains suitable chain identifiers in it. Such information isn’t present in other GROMACS formats (except perhaps .tpr, if it was generated from a PDB file with chains identified).