Re: [AMBER] ligand outside the binding site - vmd visualisation problem

From: David A Case <>
Date: Wed, 10 Jan 2018 08:19:08 -0500

On Wed, Jan 10, 2018, M. Pyrka wrote:
> I have problem with visualisation of trajectory of protein - ligand
> production in explicit solvent in VMD, namely during simulation ligand
> is suddenly going outside the binding site and after few hundreds steps
> it returns and stay there. It seems to be shifted to other picture by a
> vector. There is no rotation at the time when ligand is outside, which
> should occur for reliable simulation results. For these reasons I
> suppose this is a visualisation problem.

Try processing the trajectory file with cpptraj, and use the "autoimage"

....good luck....dac

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Received on Wed Jan 10 2018 - 05:30:04 PST
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