Hi Charles/Gabriel,
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) # loads the pdbFiles, but would they be
linked to the ensemble?? The output is not very clear if it actually loaded
two files, verbose option does not work
OUTPUT:
initCoords: still 1 unknown atomic coordinates
<protocol.InitCoordsResult instance at 0x7f31a85a0170>
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.
I am sorry for repeating the question but the output was not very
convincing.
Thanks for your time and patience,
santhosh
On Tue, Aug 27, 2013 at 9:37 AM, Gabriel Cornilescu <
[email protected]> wrote:
> It could be the psf file, maybe it needs to be re-generated from the
> structure you are working with?
>
>
> On 8/27/2013 7:24 AM, santhu kumar wrote:
>
> Hi Charles,
>
> Thanks for the tip. I am running into weird error now.
>
> The command protocol.initCoords(fileName) does not recognize any of the
> atoms while protocol.loadPDB(fileName) loads the pdb file correctly. It
> does not make sense as protocol.loadPDB internally calls initCoords [As I
> see from the code].
>
> Clip from my terminal:
> >xplor -py
> python> protocol.initCoords('model.pdb')
> PDBTool:read: atom not found in structure: MET 1 N
> PDBTool:read: atom not found in structure: MET 1 H1
> PDBTool:read: atom not found in structure: MET 1 H2
> PDBTool:read: atom not found in structure: MET 1 H3
> PDBTool:read: atom not found in structure: MET 1 CA
> PDBTool:read: atom not found in structure: MET 1 HA
> PDBTool:read: atom not found in structure: MET 1 CB
> PDBTool:read: atom not found in structure: MET 1 HB1 ..........
>
> matchInexactAtomEntry: found no match for entry 1 N
> matchInexactAtomEntry: found no match for entry 1 H1
> matchInexactAtomEntry: found no match for entry 1 H2
> matchInexactAtomEntry: found no match for entry 1 H3
> matchInexactAtomEntry: found no match for entry 1 CA
> matchInexactAtomEntry: found no match for entry 1 HA
> matchInexactAtomEntry: found no match for entry 1 CB
> matchInexactAtomEntry: found no match for entry 1 HB1 .........
>
>
> File "/home/vsvammi/programs/xplor/python/protocol.py", line 639, in
> initCoords
> unreadEntries)
> Exception: too many unreadable ATOM entries: 1231
>
> While protocol.loadPDB works perfectly. Can you please suggest whats
> going wrong. The first residue of the PDB file looks this:
>
> ATOM 1 N MET 1 27.959 25.584 17.774 1.00 0.00
>
> ATOM 2 H1 MET 1 27.970 24.816 17.118 1.00 0.00
>
> ATOM 3 H2 MET 1 28.726 26.167 17.471 1.00 0.00
>
> ATOM 4 H3 MET 1 28.248 25.201 18.662 1.00 0.00
>
> ATOM 5 CA MET 1 26.757 26.425 17.888 1.00 0.00
>
> ATOM 6 HA MET 1 26.536 26.725 16.864 1.00 0.00
>
> ATOM 7 CB MET 1 25.497 25.747 18.427 1.00 0.00
>
> ATOM 8 HB1 MET 1 24.666 26.395 18.149 1.00 0.00
>
> ATOM 9 HB2 MET 1 25.286 24.819 17.896 1.00 0.00
>
> ATOM 10 CG MET 1 25.374 25.581 19.942 1.00 0.00
>
> ATOM 11 HG1 MET 1 26.264 25.075 20.316 1.00 0.00
>
> ATOM 12 HG2 MET 1 25.329 26.565 20.410 1.00 0.00
>
> ATOM 13 SD MET 1 23.894 24.731 20.544 1.00 0.00
>
> ATOM 14 CE MET 1 24.249 24.851 22.315 1.00 0.00
>
> ATOM 15 HE1 MET 1 23.798 24.026 22.866 1.00 0.00
>
> ATOM 16 HE2 MET 1 25.321 24.814 22.509 1.00 0.00
>
> ATOM 17 HE3 MET 1 23.918 25.787 22.765 1.00 0.00
>
> ATOM 18 C MET 1 27.082 27.661 18.715 1.00 0.00
>
> ATOM 19 O MET 1 27.796 27.549 19.709 1.00 0.00
>
> Thanks
> Santhosh
>
>
> _______________________________________________
> Xplor-nih mailing
> [email protected]http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
>
>
>
> --
> Gabihttps://mywebspace.wisc.edu/gcornilescu/web/
>
>
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