Re: [AMBER] Coordinate messed up after tleap set box

From: David A Case <>
Date: Tue, 4 Sep 2018 13:37:20 -0400

On Tue, Sep 04, 2018, Simon Kit Sang Chu wrote:

> I just check the pdb (attached) and there was no gap.

Are the coordinates different in the input pdb file and the output rst7
or pdb file? You may need to add a "set default nocenter on" command to
avoid a recentering of coordinates by tleap. But at most tleap would
provide a overall translation, and would not create a "gap".

> The box dimension is stored in present.prmtop.

The coordinates in the prmtop file are generally ignored. As I
indicated in the previous email, you should look at the final line of
the $NAMEd.inpcrd file you are creating. That should be the same as
what you requested.


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Received on Tue Sep 04 2018 - 11:00:03 PDT
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