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

[Bernhard Knapp]

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)
>
>  
>