On Fri, Mar 25, 2016 at 3:06 AM, waleed zalloum
<waleed_zalloum.yahoo.com> wrote:
> However, when I visualized the producetrajectory of each cluster in VMD, I found that the cofactor (number 801) movesin the active site and outside the active site with a very high RMSD.
This sounds like a classic case of imaging artifact to me; if the
transition is not smooth, i.e. the cofactor appears to "jump", then
this is certainly what it is. In that case you need to add an
'autoimage' command before your 'cluster' command.
-Dan
> It looksthat the algorithm did not consider this cofactor in the RMS calculations, althoughit is included in the atom mask as shown in the cpptraj command.
> Also I used the same command, but I changed the atoms maskas follow, and I have got the same situation:
> clusterhieragglo crdset all-trajectories epsilon 5 averagelinkage rms :1-801&!.H=sieve 10 out cnumvtime summary summaryfile info infofile clusterout clusclusterfmt amber repout repclus repfmt pdb cpopvtime population normframe
>
>
>
> 1. Could you please advise me aboutthis situation and what is happening? The RMS of amino acids in the protein ineach cluster is good.
>
> 2. Can I re-cluster eachcluster based on the cofactor?
>
> 3. Is there any other methodthat I can use to find out what are the preferred locations of the cofactor inthe active site throughout the trajectory of 1 microsecond?
>
>
> Thank you, indeed
> Waleed
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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http://home.chpc.utah.edu/~cheatham/
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Received on Fri Mar 25 2016 - 08:00:08 PDT
