On Wed, Oct 14, 2015, Robert Molt wrote:
>
> I was hoping to please be advised where in the documentation it
> clarifies when leap chooses to add an Ho atom.
>
> In my particular case, I see Ho atoms added to non-terminal phosphates
> as well as to alcohol groups coming off of terminal ribose units. I am
> unsure what causes leap to add these to my PDB (it leaves other
> phosphates in the DNA backbone alone, just some get a Ho).
>
> These are the mysterious atoms that entered my produced PDB file that I
> formerly thought were resultant from a prepgen error.
As you know, we have serious communication problems here. Can you provide a
concrete (simple) example: give *all* the files and the *exact commands* you
are using, so that we can try to reproduce the behavior. In particular, I
don't really understand how you are creating the PDB file that has
the extra atoms.
As I have said before, LEaP is just a bookkeeping program at heart. My best
guess is that there is an atom in the library you are loading that is *not*
in the PDB file you are loading. This is the only scenario I can readily
think of where there would be atoms in an (output) PDB file that were not
present in the input PDB file. But since I don't know what libraries you are
loading, nor what PDB file you are loading, nor what commands you are giving
to LEaP, it's just really hard to give good advice.
...dac
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Received on Wed Oct 14 2015 - 13:30:03 PDT
