Dear all, I have run MD simulation using Amber12. Now I would like to check the occupancy of pi-stacking or hydrophobic interactions that the inhibitors make with the protein over the entire trajectories. I know cpptraj has the option for doing hydrogen bond analysis. Any suggestions for above mentioned interaction analysis? Can anyone please share a sample input file? Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID: saman.yousufali64.yahoo.com
saman.ali.iccs.edu
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Received on Mon Feb 22 2016 - 21:00:03 PST
