Re: (No subject)

From: a-yermakova_at_northwestern.edu
Date: Wed Jul 12 2006 - 11:46:35 CDT

('binary' encoding is not supported, stored as-is) 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). 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?
Thank you,
Anya Y

==============Original message text===============
On Tue, 11 Jul 2006 1:15:33 am +0000 Peter Freddolino wrote:

To return to the original topic... as Mark noted, it would be helpful
for us to know a bit more about your system, and in particular, what you
mean by the protein looking terrible.
What kind of MD run were you doing? And how far into the run did you get
before you got errors?
Peter

a-yermakova_at_northwestern.edu wrote:
> After the minimization, the protein (in a water box) looks terrible in VMD! And in the log file it
> keeps saying "Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.".
> Is the small cutoff value responsible for such a poor representation or can I do something else to
> change it?
>
>

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