Re: [AMBER] Active site conserve water issue.

From: David A Case <>
Date: Sat, 2 Jan 2016 10:05:29 -0500

On Sat, Jan 02, 2016, Saman Yousuf ali wrote:

> I have prepared all the necessary file for running MD. My problem is
> conserve water of my target protein active site. When I load complex
> pdb on xleap, then after saving prmtop, inpcrd and solvated complex pdb
> active site conserve water lost. I cant identify them. Can anyone please
> help me in this regard.

Are you sure they are "lost"? If waters are present in the input PDB file,
they should be there in the output files as well.

It's not clear exactly what commands you used. But try adding the following
near the top of the leap commands:

set default nocenter on

That should prevent the coordinates from being shifted when you create the
box, and might make it easier to find the original waters, which now should
have the same coordinates as they had in the original file.

...hope this helps....dac

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Received on Sat Jan 02 2016 - 07:30:03 PST
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