cluster out /home/voronkov/CLUSTER/fzd1 representative pdb average pdb averagelinkage \
clusters 10 mass rms :1-240.CA,C,N,O
I am very sorry, forgot to add the command.
-------- Пересылаемое сообщение --------
15.09.10, 22:57, "Andrew Voronkov" <drugdesign.yandex.ru>:
Dear Amber users,
I am trying to get representative or average structure from molecular dynamics trajectory. I want to use it or an ensembel of them for the docking. I am using Molprobity as one of the assessment tools. I know that it is not that straghtforward to use it for molecular models assessment, but it is just some indicator for the comparison. The strange thing that I get is that the quality of models which I get from clustering both of representative structures and average is very bad while PDB file generated from the rst file is much better. I can't understand what is the basis for this. I can understand this for average structure - when cooridnates are averaged then it s easy to move far from local minimum, but the representative structure should be not a generic structure, but one of the .rst files actually. Why it is different so much from the PDB file which I get from the .rst final file.
All three structures are in the attachment.
Sincerely yours,
Andrew
----- В пересылаемое сообщение вложены файлы: -----
CLUSTERING.zip
-------- Завершение пересылаемого сообщения --------
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Received on Wed Sep 15 2010 - 14:00:03 PDT
