RMSF and Rg Calculation of Protein & Ligand Complex

User discussions
1

GROMACS version: 2021.2
GROMACS modification: No

Hello all,

I have carried out an MD simulation for protein & ligand complexes. I’ve properly done RMSD calculation of the complexes with “gmx rms” command by selecting two separate groups like “Protein” and “Ligand” on the command prompt. And then, I wanted to repeat the same pathway for Rg and RMSF analysis of my complexes but I was just able to select individual protein or ligand since no second option popped up to select the other group on the prompt, so I was unable to combine the protein and the ligand in which I’ve done for RMSD analysis. I can see in the literature that researchers have successfully completed Rg and RMSF analysis of complexes but I am not sure if I am missing some point and could not carry out these calculations for my work.

I’ve used the following commands for the calculations:

RMSF: gmx rmsf -f md_0_10.xtc -s md_0_10.tpr -o rmsf.xvg -res
Rg: gmx gyrate -s md_0_10.tpr -f md_noPBC.xtc -o gyrate.xvg

Any help would be appreciated, thanks in advance!

2

Hi,

gmx rms calculates the root mean square deviation between the simulated structure ( xtc file) and a reference structure (tpr file).

gmx rms -f {}.xtc -s {}.tpr -o
ask for a group for least square fitting and one group for rmsd calculation.
to get the rmsd values for two group (e.i protein and ligand) one has to use the option -ng

An equivalent option does not exist for gmx rmsf and gmx gyrate.
One has to run the tools for each molecular system independently.

If one is interest to have fluctuation of two different molecules without fitting them independently to a reference, one can use the option -nofit and take care that trajectory and reference structure match.

I hope that helps.
\Alessandra

3

Hi Alessandra could you pls give us more information how can we create new index group for complex? and and how can we use -ng command?

4

Hi,
to create index file you can use the tools: gmx make_ndx (https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html ) or gmx select (https://manual.gromacs.org/current/onlinehelp/gmx-select.html).
-ng is an option of gmx rms and correspond to the “number of groups to compute RMS between”
Alessandra