[AMBER] fatty acid ligand comes out of binding site during md.

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Sat, 20 Jan 2018 13:43:11 +0000 (UTC)

Dear All,I have performing docking of two different fatty acids with protein (91 residue length) separately. After that I have run 10 ns simulation of these docked complexes using amber16. To perform analysis,  I reimaged trajectories first using autoimage command via cpptraj and then I have extracted 100 frames out of 10000 frames using folllowing command;parm  nowater.myristic.prmtop
trajin  *.nc 1 10000 100
trajout nsltp-myr-100frame.ncWhen I visualized these extracted frames, I have observed that one fatty acid comes out of protein cavity after 9ns. Image attached below.
Any help anyone could offer to solve this issue would be greatlyappreciated.


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(image/png attachment: myristic-protein.png)

Received on Sat Jan 20 2018 - 06:00:04 PST
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