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----- Forwarded message from Denis Volkov <> -----
Date: Thu, 11 Sep 2003 14:15:18 +0400
From: Denis Volkov <>
X-Mailer: The Bat! (v1.52f)
Organization: IBCH
To:
Subject: Re: model_refinement
Hello,Oliver
Thank you for fast answering! :)
No i didn't test a quality of templates course i
used 4 structures
as a templates so its difficult to do it. Alignment
I manually adjust
so it's not a origin of fault. I look at the model
again and think
it's not so bad as I said. But a problem is more
global:
A similarity with templates is no more than 20%. A
great deal of
mismatches are in loop origin so it's not so
bad...but can i do a good
model with so low similarity? As I said I use
Charmm, I used it to investigate
protein-protein interactions. I used Modeller model
to investigate
enzyme-substrate and enzyme-inhibitor interaction.
But after MD a
structure was a great deal disturbed. Is it a
problem of low
similarity or as you said its not good to use MD
with models maid by
Modeller?
Also I've another question: earlier I used Windows
version of
Modeller and everything was OK, but now I run
Modeller on Linux and
have some problem. When I used sequence-search
routine it runs for
some time (~30-40 min) but then terminated. In log
file there is
nothing interesting: chains libraries were opened
two times. First
times it takes 20Mb of memory, second time ~200 Mb
and then it
terminated. So the problem is a memory usage as I
think. I looked
through archive and find out that it's a common
problem. I checked my
top-files and system config (stack size) and
everything is good. I've
got 500 Mb RAM but half of it utilized by X-Windows.
So may be i
should run some Modeller routines without running X ?
Thanks in advance
Denis Volkov
Enzyme Laboratory,IBCH RAS
--
Best regards,
Denis
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