Dear Dan,
Thank you for your reply regardingthe clustering problem. I tried the autoimage command with different anchor moleculesof my system according to your suggestion. I got the same situation, goodprotein rms and the cofactor moving in the active site. The following are my commandsfor cpptraj:
Autoimage
rms first mass :1-801&!.H=
cluster C1 hieragglo crdsetall-trajectories epsilon 5 averagelinkage rms :1-801&!.H= sieve 10 outcnumvtime summary summaryfile info infofile clusterout clus clusterfmt amberrepout repclus repfmt pdb cpopvtime population normframe
I tried all the following separately:
1. Increase and decrease the epsilon value
2. Use average-linkage and complete linkage
3. rms only on protein, and then nofit in the cluster command
4. I tried rms at the cofactor and then nofit in the clustering
5. After running number 4 above, I re-clustered (based on thecofactor)the most populated cluster as follow, with nofit:
cluster C1 hieragglo :801 crdsetall-trajectories epsilon 6 complete rms nofit sieve 10 out cnumvtime summarysummaryfile info infofile clusterout clus clusterfmt amber repout repclusrepfmt pdb cpopvtime population normframe
After the second cluster I havegot 974 clusters.
Do you have any explanation whatis happening with my system. Please, do you have any suggestions to analyse mysystem
Thank you, indeed
Waleed
======================================== Waleed A. Zalloum, BSc, MSc, PhD, MRSC, ACSAssistant professor of medicinal chemistry and drug discovery- Structural biology American University of Madaba Amman-Jordan E-mail:
waleed_zalloum.yahoo.com========================================
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Received on Mon Apr 18 2016 - 11:30:03 PDT
