Forwarding to list.
----- Forwarded message from Denis Volkov <themelon(a)yandex.ru> -----
Date: Mon, 8 Sep 2003 17:41:54 +0400
From: Denis Volkov <themelon(a)yandex.ru>
To: Modeller Caretaker <modeller-care(a)salilab.org>
Subject: Re: Fwd: Re: model_refinement
Thursday, September 04, 2003, 12:16:20 AM, you wrote:
MC> ----- Forwarded message from Oliver Hucke <ohucke(a)u.washington.edu> -----
MC> Date: Tue, 02 Sep 2003 10:03:00 -0700
MC> From: Oliver Hucke <ohucke(a)u.washington.edu>
MC> To: Modeller Care <modeller-care(a)salilab.org>
MC> Subject: Re: model_refinement
MC> Hi Denis,
MC> did you compare the quality of the structure calculated with modeller
MC> with that of the template(s)?
MC> If the quality of the model is really worse something might be wrong
MC> with your alignment. Did you do the manual adjustment of the input
MC> alignment on basis of the analysis of the quality of the first models?
MC> This usually helps a lot.
MC> I do not think that it is necessary to use charmm or another external
MC> molecular mechanics package to improve the quality of your model.
MC> Modeller actually uses (an older version of) the charmm force field for
MC> the molecular mechanics part of the optimization.
MC> Modeller Care wrote:
>>------ Forwarded Message
>>From: Denis Volkov <D.Volkov(a)artcustoms.ru>
>>X-Mailer: The Bat! (v1.52f)
>>Reply-To: Denis Volkov <D.Volkov(a)artcustoms.ru>
>>X-Priority: 3 (Normal)
>>To: modeller <modeller_usage(a)salilab.org>
>>I successfully used Modeller to model unknown protein. Now I'd like
>>to sent my model to Protein Data Bank. So i checked my structure
>>using Procheck and find some problems, namely some bad contacts,etc.
>>In order to clean a structure i used Charmm program for energy
>>minimization. But after it i obtain structure with bad angles and
>>bond lengths. Can anybody know how to clean a structure well for
>>PDBank and what programs should be use for it.
>>Thanks in advance
>>Enzyme Laboratory,IBCH RAS
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
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
Enzyme Laboratory,IBCH RAS
----- End forwarded message -----