Forwarding to list.
----- Forwarded message from Denis Volkov themelon@yandex.ru -----
Date: Thu, 11 Sep 2003 14:15:18 +0400 From: Denis Volkov themelon@yandex.ru X-Mailer: The Bat! (v1.52f) Organization: IBCH To: modeller-care@salilab.org 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