Hi Amber Users,
Greetings.
Can someone please let me know how to visualize and infer the output file
(ClusterMerging.txt)
from ptraj-cluster program ?
I just fired up the file with xmgrace and I don't get much.
FYI:
I have run a MD simulation of protein-ligand complex and used cluster
program from ptraj for getting representative and average structure of the MD
run.
I used averagelinkage method for clustering. Clustering process went well. I
used the
following command in ptraj
cluster out mk2mdrun all amber representative pdb average pdb averagelinkage
sieve 10 clusters 5 rms mass :1-300
Thanks in advance.
Senthil Natesan
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Received on Wed Sep 01 2010 - 14:30:03 PDT
