From: Basheer Subei (
Date: Fri Aug 22 2014 - 19:35:18 CDT

Hello all,

In the Nanopore Tutorial
(forgive me if this is the wrong mailing list), in section 3.6, the first
step is to combine both the SiN nanopore and the dsDNA by running the
script "combine.tcl. However, the script uses the unequilibrated structures
"dsdna.pdb" and "sin_pore_charges.pdb" (i.e. *before minimization and

Is there a reason why the tutorial doesn't just use the
already-equilibrated structures from the previous sections 3.1 and 3.3? I
just want to make sure that there isn't some reason unknown to me why I
can't just use the equilibrated dsDNA and SiN nanopore and combine them.
(of course, I'll take care to remove the water and ions from the DNA before
combining it with the nanopore and then minimize and equilibrate the
combined system as normal)

Am I on the right track? Thanks in advance!

- Basheer Subei

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