[gmx-users] Diagnosing + system blowing up

Justin Lemkul jalemkul at vt.edu
Sat Jul 28 22:44:57 CEST 2012

On 7/28/12 2:47 PM, Shima Arasteh wrote:
> Dear Mark, Thanks for your suggestions.
> Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all! However I see this pair in the [pairs] section of topology !
> So I can get the result of an inappropriate bond interaction here! Correct?
> Now I think it's not necessary to go through the diagnosing steps any more! :-(
> What is my duty right now?!
> Is this problem supposed to be fixed in the .pdb file? What's wrong with the pdb file? What about erasing the unexpected bond interactions in topology file?

You'll need to back up and provide more information here.  I recall our 
discussion several weeks ago about this formylated valine problem, which was 
solved by creating a special residue called FVAL.  If you created a correct .rtp 
entry like I described, this shouldn't be happening.

If you're proceeded some other way, you will have to specify exactly what you've 
done up to this point.  This may require snippets of relevant residues in 
coordinate files, .rtp entries, etc.  Without this information, everything I've 
seen thus far is a jumbled mess that is nearly impossible for anyone on this 
list to troubleshoot.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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