MBG wiki | RecentChanges | Blog | 2021-09-24 | 2021-09-23

Calculation of rmsd from the starting structure

If you've used carma to remove translations-rotations, then you already have seen a plot of the evolution of rmsd from the starting structure vs. time.

A more complex example for a protein with 4 segments (A, B, C, D) is :

carma -fit -atmid "ALLID" native.psf native.dcd
mv carma.fit-rms.dat ALL.dat
carma -fit -atmid "ALLID" -segid " A   " -segid " D   " native.psf native.dcd
mv carma.fit-rms.dat AD.dat
carma -fit -atmid "ALLID" -segid " B   " -segid " C   " native.psf native.dcd
mv carma.fit-rms.dat BC.dat
carma -fit -atmid "ALLID" -segid " A   " native.psf native.dcd
mv carma.fit-rms.dat A.dat
xmgr ALL.dat AD.dat BC.dat A.dat

giving something like :

 Calculation of rmsd from the starting structure (xmgr)

You can do a far more gentle job via the xplor scripting language (try to understand the atom selection syntax) :

structure @native.psf end

coordinates disposition=comp @starting.pdb

evaluate ($first = 0)
evaluate ($step  = 1)

evaluate ($current = $first)

read trajectory

asci=false
input=native.dcd
begin=$first
skip=$step
stop=2000000000
end

set display=sidechain.rmsd end


while ($status # "COMPLETE") loop traj


coor fit selection=((resid 8 or resid 26 or resid 52 or resid 22 or resid 38\
                    or resid 45 or resid 48 or resid 37 or resid 15 or\
                    resid 19 or resid 41) and not (name CA or name C or\
                    name O or name HN or name HA or name N) and not hydrogen\
                    ) end

coor rms selection=((resid 8 or resid 26 or resid 52 or resid 22 or resid 38\
                    or resid 45 or resid 48 or resid 37 or resid 15 or\
                    resid 19 or resid 41) and not (name CA or name C or\
                    name O or name HN or name HA or name N) and not hydrogen\
                    ) end

evaluate ($rms = $RESULT)

display $current $rms



evaluate ($current =$current + $step)

read trajectory next end

end loop traj

stop

where starting.pdb is a PDB containing the initial coordinates of the solute (after PSF generation).