[gmx-users] Re: Re: Re: Re: problems with some calculated trajectories

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Thu Jun 25 13:44:22 CEST 2009

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
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


>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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