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

From: Daniel Roe <>
Date: Tue, 23 Jan 2018 11:36:47 -0500


I'm not clear on what your issue is. If the ligand has come out of the
binding pocket, it's out. Is that a problem?


On Sat, Jan 20, 2018 at 8:43 AM, Saman Yousuf ali
<> wrote:
> 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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Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Jan 23 2018 - 09:00:02 PST
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