Repeating sequence of the residue numbers in the RMSF output

[ka123]

GROMACS version: 2020.2
GROMACS modification: No
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Hi,

I’m currently doing a protein simulation (protein made of 3 chains) using gromacs, and since I’ve been getting enough data to analyze the protein structure, I ran RMSF command to get the RMSF (C-alpha) values for the protein residues as follows:

gmx_mpi rmsf -f md_1_113_concat_protein.xtc -s md_0_1.tpr -o rmsf_per_res_calpha_113_800ns.xvg -e 800000 -res

With -res option attached, I know that I’m getting the RMSF for each residue of the protein and I actually see that those values are given in the output file, rmsf_per_res_calpha_113_800ns.xvg. However, on the same file, I also see the repeating sequence of the residue numbers (three times, to be more clear), each time with different RMSF values, like the images attached below (images only showing parts of the file. The file basically repeats residue number 27-1147 “three” times):

More details about the protein I’m simulating are:

• It is made of three chains (chain A, chain B and chain C)
• Each chain is made of residues 27-1147 (27, 28, …1146, 1147).

The protein is made of 3 chains and the sequence of the residue numbers is repeating three times in the output .xvg file makes me suspect that each repeating sequence is for each different chain of the protein, but I’m not fully sure about this.

I just want to know if these repeating sequence of numbers are for the residues of each different chain, and if so, would it be in the order of chain A, chain B and chain C or some other order.

Thank you for your help!

Best,
Karin

[alevilla]

Hi,

the order of the residues is the same order that you have in the topology file.
Using the option -s tpr file, the gmx tools take the information on the system topology (ref structure) from md_0_1.tpr.
Best regards
Alessandra

[ka123]

Hi Alessandra,

Thank you for your response.
Now it got more clear to me which file I should check to get the information I want.

I just opened the .tpr file using the command: [gmx dump -s topol.tpr] to see the residues order.
It turned out it has the residue information in the order of: [Chain A] residue 27 to residue 1147 → [Chain B] residue 27 to residue 1147 → [Chain C] residue 27 to residue 1147.

Just to get a final confirmation from you, this should mean that the gromacs RMSF with -res option gave me the RMSF of the residues of each chain in the order of ChainA, Chain B and Chain C (all from 27 to 1147), is it correct?

Thank you so much for your help!

Best,
Karin

[alevilla]

yes.
Alessandra

[ka123]

Great, thank you!

Best,
Karin