Hello Santhos--
>
> I was able to successfully load the pdb files using both loadPDB and
> initCoords [i generated a psf file using pdb2psf and since the psf would be
> the same for all the ensemble simulation members I think thats OK].
>
> But I am not really sure if its doing the right thing. Just to be clear of
> the question:
> I want different ensemble members to have different starting structures.
> Here is the snippet of the code, my reason for confusion in comments :
>
> protocol.initRandomSeed()
> protocol.initParams("protein")
> ensembleSize = 2
> pdbFiles = ["model0.pdb","model1.pdb"] # these two files should be the
> starting structures
>
> esim = EnsembleSimulation("ensemble",ensembleSize)
> memberIndex = esim.member().memberIndex() # this makes memberIndex = 0
> protocol.initStruct('model.psf') # the default psf file
> protocol.initCoords(pdbFiles) #
close: please instead use
protocol.initCoords( pdbFiles[memberIndex%2] )
>
> The same code as Charles has wrote :
> protocol.initCoords(pdbFiles[memberIndex%2]) # using 2 structures,
> memberIndex%2 would always be zero as memberIndex =0, means the code loads
> only one file.
No. memberIndex is 0 or 1 for a 2-membered ensemble. To better see
what is going on, you can enable output for those having non-zero
memberIndex by adding the flag
-thread_filename thread.out
to the xplor command invocation. You will then have files for each
non-zero ensemble member ion your directory.
best regards--
Charles
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