Crystal Structure Analysis

Date: Tue Feb 27 2007 - 12:02:23 CST


I am running a simulation of a collagen-like peptide know as EKG with
the PDB entry of 1QSU I have been able to set up this simulation and
run it. But now i want to be able to analyze the data from it which
are water bridges and distances between the peptides. But the problem
is that my simulation only has 2 collage peptides (image) and that i need
to include more peptides to do the full analysis.

You can see the gaps of water in the top left corner and the bottom
right. This is where the bottom and top of the peptide belongs.

I was wondering how i can make a larger crystal using this crystal
unit cell using VMD or other software.

many thanks
-Pedro Borkowski

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