Re: (No subject)

From: Peter Freddolino (
Date: Wed Jul 12 2006 - 14:15:06 CDT

Could you post a screenshot of what you're seeing? Or your pre- and
post-solvation psf/pdb files?
Also, what type of representation are you using to view the protein?
Peter 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). 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
> 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?
> ===========End of original message text===========

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