On Thu, Apr 13, 2017, Li, Wen wrote:
>
> My RNA molecule has three dimensions of 200, 160, 180 Angstroms, I did
> the steps as shown below. From the final pdb with waters, the water box
> contains only a portion of the molecule, and a long pole consisting
> of only H atoms. Due to the email size limitation, I can't attach an
> image to show the pdb.
This is indeed an odd report. How big is the pdb file? Are you allowed
to share it? Somehow, we would need to be able to try to reproduce the
problem. I don't know of any problems with solvateBox related to the size
of the system, and 100 Ang. is not an unusally big molecule.
One thing possibly to try first: execute solvateBox before addIons, not after.
Probably won't help, but is worth a try, and might help narrow down the source
of the problem.
....dac
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Received on Thu Apr 13 2017 - 07:30:03 PDT
