On Fri, Sep 18, 2015, Kalenkiewicz, Andrew (NIH/NICHD) [F] wrote:
>
> I'm trying to set up a system with a protein that binds GTP and GDP
> nucleotides. However, the magnesium ions that coordinate the phosphate
> tails keep getting misplaced in the final system. I.e. they are nowhere
> close to the nucleotides even though the input PDB coordinates are
> correct (the output coordinates are somehow changed in the final
> system). I've attached my corresponding leap script for reference. If
> you need other files to troubleshoot this issue let me know, but since
> there are quite a few involved I won't send them right away in case it's
> something obvious in the leap script.
Is it just the Mg ions that are misplaced, and nothing else?
Try this: manually combine all your pdb file into a single one, and use
loapdb to load that; avoid using the "combine" command in LEaP. It's
actually unclear from the documentation exactly what the "combine" command
is supposed to do with coordinates. If "combine" is not doing what you
might expect it to do, we should indicate that in the documentation. It's
also possible that this is a fix-able bug, if the problems happen only
with monoatomic ions.
(Perhaps worth trying: add "set default nocenter on" to your script. But I
don't think this will help.)
....dac
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Received on Fri Sep 18 2015 - 12:00:03 PDT
