The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope,
T-cell receptor alpa, T-cell receptor beta).
What you can see in
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
is exactly the same angle. The two MHC chains "jump" away from each
other and from the T-cell receptor. I have already simulated some of
these complexes before with slightly different amino acid sequences but
with an overall similar structure and this "jumping" never occured.
I did the following conversion:
trjconv -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -o
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -n index.ndx -pbc nojump
-novel -fit progressive -skip 10
and the rmds calculation with
g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o
rmsd.TcrCdrs.noJump.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 7
but also if I calculate the rmsd directly from the trr-file the jumps
are inside and the same as from the xtc file without "-pbc nojump"
g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -s
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o
rmsd.TcrCdrs.fitpMHC.FromOriginalTRR.xvg -n index.cdrsAndStrands.ndx -ng 7
cheers
Bernhard
Today's Topics:
1. Re: Re: Re: problems with some calculated trajectories
(Tsjerk Wassenaar)
2. Re: Re: Re: problems with some calculated trajectories
(Mark Abraham)
3. RE: Re: Re: problems with some calculated trajectories (Berk Hess)
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