Many thanks for the note. I wanted to avoid superimposition but this should
work for me.
Best,
Mish
On Tue, Jul 21, 2015 at 3:05 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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 Wed Jul 22 2015 - 08:00:04 PDT
