On Thu, Jan 31, 2013 at 9:16 PM, Joe Passman <joepassman.comcast.net> wrote:
>
>
>
>
>
> Hi all,
>
>
> I am interested in running a minimization on a lengthy peptide. I would
> like to use a cubic solvation box for periodicity. I have been encountering
> some problems as I change the box length. At 20 ang, the box seems to
> small, and I am worried that conformational changes could lead to
> interactions with the neighboring replica. If I make the box bigger (i.e.
> box length = 60 ang), the boxes of water look like they are stacking on top
> of each other.
>
>
> I am running the tleap script from a python subprocess. Originally, I
> speculated that this could lead to some problems. However, I have manually
> solvated this system, and the same thing happens. My tleap script is below:
>
>
>
> #!/bin/bash
> source leaprc.ff12SB
>
>
> l100 = loadpdb lambdaN_100.pdb
> solvatebox l100 TIP3PBOX 20
> savepdb l100 wb_lambdaN_100.pdb
>
> quit
> !
>
>
> To sum, I am searching for a way to solvate a long peptide.
>
In addition to what Dave said, I'll ask what the _end_ goal of all this is.
Do you plan on running dynamics with Amber -- that is, do you ultimately
plan on making an Amber topology file?
If all you wanted to do was solvate your system to generated a solvated PDB
file, then may I suggest using another software like packmol instead? Such
programs were designed specifically for that purpose, whereas tleap
implements that behavior mainly to aid in generating topology files.
Also, I suspect that what you may be seeing with the large box size is as
much a limitation of the PDB file as it is a tleap bug -- the format
requirements of the PDB file is very strict, and if any of the numbers are
too large, you can get strange behavior with different parsers.
What happens if you actually generate a topology file with the 60-Angstrom
buffer and visualize that instead? Do you still get the very weird
behavior?
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Feb 01 2013 - 05:30:03 PST
