Tutorial-l Mailing List

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Sat Aug 23 2014 - 13:16:22 CDT

Hi Basheer,

Using the already equilibrated DNA is a good idea. I think the
tutorial was written so that you could skip some parts and each
section would be self-contained. But there should be no problem using
equilibrated DNA, assuming that the force field used doesn't make
native DNA structures fall apart, which was a problem for older CHARMM
and Amber force fields
(http://dx.doi.org/10.1529/biophysj.106.097782).

On the other hand, for the SiN, you should be careful to maintain the
atomic positions in the original crystal structure when starting from
an "equilibrated" SiN structure. It might be easy, by mistake, to grab
the last frame of your equilibration and use this last frame to define
the positions to which the atoms are restrained. The SiN force field
is intended to be used with the atoms restrained to the crystal
structure. Given that the structure is restrained anyway, there might
not be much of a need to equilibrate SiN.

Note that the SiN force field hasn't been particularly well calibrated
for many purposes — it was only designed to reproduce the dielectric
constant of SiN. Binding of ions or DNA may not be accurate. The SiO2
force field has undergone more testing
(http://dx.doi.org/10.1021/jp063896o). For SiO2, you need to be
careful to maintain the restraint positions to the last frame of the
annealing (where a different force field is used).

Jeffrey Comer, PhD
Assistant Professor
Department of Anatomy and Physiology
Kansas State University
College of Veterinary Medicine

On Sat, Aug 23, 2014 at 12:43 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Hi Basheer,
>
> Using the already
>
> Jeffrey Comer, PhD
> Assistant Professor
> Department of Anatomy and Physiology
> Kansas State University
> College of Veterinary Medicine
>
>
> On Fri, Aug 22, 2014 at 7:35 PM, Basheer Subei <basheersubei_at_gmail.com> wrote:
>> 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 equilibration).
>>
>> 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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