Justin,<br><div class="gmail_quote"><br>Sorry again for the delay.<br><br>I've finished minimise my system with the CG algorithm in double precision ( after steep minimisation )<br>but the output was<br><br>Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>but not to the requested precision Fmax < 0.1<br><br>Than I've tried to equilibrate this system with the NVT conditions and obtain old error about collapse of my system :)<br><br>
šI've found logs of both minimisation ( both of the logsš were very big I've coppied only end part of those output data )š and attach it to this topic.<br><br>Also I've run minimisation in vacuum as you've told me but this results would be aviable tomorrow.<br>
<br>Could you tell me whats exactly wrong with that system and is there possible ways to fix the problem?<br><br>Thanks for help<br><br><br>James<br><br><div class="gmail_quote">31 ÍÁÒÔÁ 2012šÇ. 22:05 ÐÏÌØÚÏ×ÁÔÅÌØ James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span> ÎÁÐÉÓÁÌ:<div>
<div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Justin,<br><br>Sorry that I can't provide you with such information now because that data have been left in my lab workstation. Tomorrow I'll find all this logs and attach it to this topic. Also I've run more properly CG minimisation ( EMtool=0.01) in double precission mode. I'll check this results too and attach all logs here. <br>
<br><br>Many thanks again for help<br><br>James<br><br><div class="gmail_quote">31 ÍÁÒÔÁ 2012šÇ. 21:57 ÐÏÌØÚÏ×ÁÔÅÌØ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> ÎÁÐÉÓÁÌ:<div>
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<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Justin,<br>
<br>
31 ÍÁÒÔÁ 2012 Ç. 18:18 ÐÏÌØÚÏ×ÁÔÅÌØ Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> ÎÁÐÉÓÁÌ:<div>
<br>
<br>
<br>
š šStart by inspecting the initial configuration in the vicinity of<br>
š šthese atoms. Something is likely clashing here.<br>
<br>
<br>
Yes, I've checked both of the proteins and found that the problem atoms were situated exactly in the docked region of the both proteins. So It seems that there are some clashes between atoms in the docked site. By the way this site of the first protein ( Receptor) consist of 2 flexible loops and the rigid helix from the second protein. ( fragment of G-protein) Might the energy minimisation solve this problem generally ? ( e.g by means of CG minimisation to very low forces aplied on atoms). Is there any possible ways to change conformation of the flexible loops during minimisation\ equilibration phases without aplication of any external forces?<br>
<br>
</div></blockquote>
<br>
Proper EM should resolve such clashes, but under normal circumstances that should have happened already. šYou may have to do EM in vacuo before adding any solvent to allow for proper resolution of clashes. šI'm only guessing at this point. šI have asked twice for the output of your previous EM attempts, which would give me a much better idea of where things stand. šSince you haven't answered those questions, I'll leave it up to you to try to resolve. šGood luck.<span><font color="#888888"><br>
<br>
-Justin</font></span><div><div><br>
<br>
-- <br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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