[Chimera-users] MD trajectory analysis

George Tzotzos gtzotzos at me.com
Mon Oct 10 13:54:02 PDT 2016

My task is to identify ligand interactions with protein residues throughout an MD trajectory. I thought of something along the lines 
sel ligand z<3.5 #for vdW interactions, etc. 

I don’t think this can be done using the MD movie interface but I may be wrong.

I then tried the following:
1. sel protein/hold selection steady
2. sel ligand
3. calculate occupancy (MD Movie/Analysis)
4. Chimera/select/clear selection
5. turned the Volume Viewer to mesh/level2.

What I obtained is a mesh grid enclosing solid surfaces (see attached snapshot). I’m not able to get rid of these surfaces? 

I think that the problem ma be in step 2 above (sel :ligand). My ligand is N,N-Diethyl-meta-toluamide. Should I select the aromatic ring part separately of the amide part, run the above process and then repeat selecting the amide part? 

I also tried MD movie/Analysis/Residue interaction network, first selecting the ligand. 

The results I obtained are not satisfactory. 

Is there a better way of dealing with my problem?

Thanks in advance for your kind help


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