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

[Erik Marklund]

Bernhard Knapp skrev:
>
> 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
>
As Tsjerk stated earlier, fitting prior to jump-removal can mess up the 
trajectory.  Try without -fit. g_rms will superimpose the structures for 
you anyway.
> 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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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys