Re: (No subject)

From: LEWYN LI (
Date: Wed Jul 12 2006 - 14:00:37 CDT


On Wed, 12 Jul 2006, wrote:

> I am working with hemagglutinin (a protein of 1602 residues, ~300kD). In fact, the protein was
> already misshaped right after I solvated it in the water box (even before the minimization).

         This is really weird! Solvating a protein in a water box usually
just means you are adding the protein coordinates, resid, atom number etc.
to the water box pdb file and removing the water molecules that overlap
with the protein. By definition, this cannot change the shape of the
protein. How are you solvating the protein? Have you looked at the
protein before solvation? Is the water box big enough to contain the
whole protein? You could print out the coordinate file right after
solvation and look at it in something like emacs or vi or any text
editor/word processor you are familiar with. If something has gone wrong
during solvation, it might show up in the coordinate file.

> I have
> gone through the tutorial and followed the instructions. By "looking terrible" I mean that many
> structures (s.a. helices) are represented simply as lines. If you take those lines away, there
> wouldn't be much left of the protein. I think that means that that information is simply missing -
> because if I try to calculate distances on one of those "lines", nothing shows up.
> What am I doing wrong?

         Mm ... I don't know what might be going on. I presume you are
looking at the solvated structure in VMD? If, as you suspected, the
information is simply missing, the coordinate file will reflect this. So
I suggest that you look at the coordinate file before and after solvation.

         Hope this helps!


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