By the way<br><br>Today I've examined in vacuum minimisation outputs more carefully ( watching in vmd trr ) and found that conformation of the loops in the docked regions were changed after long CG minimisation.<br><br>
Then I've resolvate my system and add ions and run STEEP minimisation of that system.<br><br>After this I've decreasing integration step to the from 0.001 to 0.0001.<br><br>Unfortunatelly the error was the same<br>
<br>starting with the LINK warnings like<br><br>Step 0, time 0 (ps)š LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.002089, max 0.082711 (between atoms 1387 and 1388)<br>bonds that rotated more than 30 degrees:<br>
šatom 1 atom 2š angleš previous, current, constraint length<br><br><br>and ending with the exploiding of my system as well with the eror like<br><br>step 29: Water molecule starting at atom 42310 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br><br><br>Also I've changed COM groups ( to the System value in one case as well as placing the second protein group to the common group with the first protein and membrane in the second case ). But the result was the same.<br>
<br><br>Is there anyš suggestions or should I start with another conformation of first protein ?<br><br><br>James<br><br><br><br><div class="gmail_quote">2 ÁÐÒÅÌÑ 2012šÇ. 9:56 ÐÏÌØÚÏ×ÁÔÅÌØ James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>></span> ÎÁÐÉÓÁÌ:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Justin,<br><br>Thanks again for attention to my problem.<br><br><br>I've checked my system and found that the problem was exactly in the 1388 atom ( wich is not properly minimized in accordance to the log files). This atom is the Cb atom of Gln residue wich placed between one loop of the protein and docked alpha helix of the peptide. Theš surrounding of that atom ( It's likely that other intracellular loops of the receptor as well as long N term protect this side chain to rotate during the minimisation ). When I've checked pdb files produced by exploding system I've found that some atoms ( from that loops) were moved from the pereodic boundaries ( I've obtain very big system as the conseqyence surrounding by some single atoms. So it all look like as big artifact :) )<br>
<br>So it seems that I need to use slightly different initial conformation of the receptor because minimisation could not to resolve such crushes.<br><br><br>Thanks again<br><br><br>James<br><br><div class="gmail_quote">
1 ÁÐÒÅÌÑ 2012šÇ. 21:37 ÐÏÌØÚÏ×ÁÔÅÌØ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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"><div><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<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 ( the step minimisation log was very big I've coppied only end part of this output data ) šand attach it to this topic.<br>
<br>
</blockquote>
<br></div>
Both of these log files indicate that EM was likely fine. šFor future reference, the following sections were all I was asking for all along:<br>
<br>
>From CG:<br>
Potential Energy š= -5.96597537065782e+05<br>
Maximum force š š = š1.42815783701700e+02 on atom 1388<br>
Norm of force š š = š1.58963638409829e+00<br>
<br>
>From steep:<br>
Potential Energy š= -5.7233788e+05<br>
Maximum force š š = š7.0209003e+02 on atom 1388<br>
Norm of force š š = š1.1310696e+01<br>
<br>
CG gives you the better minimization, overall, as expected. šAtom 1388 bears the maximum force, but it is not of problematic magnitude.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also I've run minimisation in vacuum as you've told me but this results would be aviable tomorrow.<br>
<br>
</blockquote>
<br></div>
It's probably not necessary, after all. šI was guessing at that point based on incomplete information.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Could you tell me whats exactly wrong with that system and is there possible ways to fix the problem?<br>
<br>
</blockquote>
<br></div>
As I've said before, the only strange thing you seem to be doing is with your comm-grps. šChange this setting to "System" and see if it runs. šOtherwise, I can find no reason for the immediate instability. šIf it still crashes, perhaps decrease the time step for the initial equilibration.<div>
<div><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
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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>
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