RMSD of a CHARMM-GUI Membrane Protein Relative to Crystal Structure Inquiry?

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question:

Hello, I membrane implanted a protein via CHARM-GUI and am RMSD analyzing this and although the RMSD relative to the structure present in the minimized, equilibrated system via the command:

gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns

from tutorial-1 exhibited correct low RMSD values of less than 0.2, the subsequent RMSD analysis versus the crystal structure via the command:

gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns

exhibited all RMSDs above 4.5.

Are these high values due to an inconsistency within the CHARM-GUI generated em.tpr?

Thanks:)

2

RMSD is an extrinsic property. Larger structures will have larger values. You may have long loops that change over time and cause a large RMSD. You need to watch the trajectory to see what happens as the RMSD increases over time.

3

Hi Justin thank you for your kind update:).

Yes I had read this response from a similar inquiry here but was confused because of my original RMSD relative to the equilibrated system exhibiting low RMSDs. OK I will update myself on this trajectory over time if I can, thanks again:)

4

Hi Justin yes I inspected the trajectory as suggested and yes the loops from this transmembrane protein are highly dynamic precipitating that above 4.5 RMSD. (And correction * my first RMSD was assessing the `corrected trajectory´ hence no confusion.) Thanks again:)

5

Hi Justin I computed my rmsd_xtal.xvg for my MODELLER loop modeled non-CHARMM-membraneous model and its values were 0.1-0.3 unlike my higher CHARMM-GUI values
from above, is this because of the membrane influence via CHARMM-GUI? Thanks if you
know:)