Re: [AMBER] Unchanged coordinates in leap

From: David A Case <>
Date: Tue, 21 Jul 2015 07:05:50 -0600

On Tue, Jul 21, 2015, mish wrote:
> I would like to know if there is some way to keep protein coordinates
> unchanged when adding water box in tleap (in AmberTools 15). "set default
> nocenter on" works fine when I am not adding any water box (coordinates of
> complex.pdb written by tleap are unchanged). However, if I use SolvateBox
> or SolvateOct, leap changes protein coordinates slightly.

I'm not sure that there is any (easy) way to avoid this, given the way
the code in solvateBox works. But you should be able to use cpptraj to
superimpose the protein coordinates you get from your savePdb command back
to the original positions that were in protein-wt.pdb. Would that suit
your needs?

This is really a deficiency in the "nocenter" option in LEaP. I'll enter a
bugzilla note about this, but I'm not sure what the best fix is.

Thanks for the report....dac

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Received on Tue Jul 21 2015 - 06:30:02 PDT
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