> Can you provide more information? What makes you think that sqm ran out
of
> memory? Why at atom 65?
In the included I/O file (nohup.out) shows the console output. At the end
of the file there is:
~~~
Info: the number of the path atoms exceeds MAXPATHATOMNUM(2480000) for
atom[65],extend the size and reallocate the memory automatically
Info: the number of the path atoms exceeds MAXPATHATOMNUM(2485000) for
atom[65],extendKilled
~~~
Which is why I think it failed at atom 65.
> 282 atoms is a very large number to be using with
> antechamber and sqm: are you sure that you should not be breaking your
> molecule into fragments?
>
> You might post your sqm.in file (or input pdb file). Without more
> information, people on the list cannot be of much help here.
>
> ...dac
Here is the .pdb: http://pastebin.com/raw.php?i=bP2Dfd3Z
I am new to this so I am not sure of anything to be honest. I wasn't aware
I could break the molecule into fragments.
I could break this molecule into the bowl shapes, the n-hexanes attached to
the bowls, and the pentane linker.
My question is how would I deal with the bond connections? I.E. Let's say
we have ethane and I want to fragment it in half with the two carbons.
Would I make it CH4? Or would I do CH3 anion/carbocation? What would the
input .pdb look exactly?
Thanks a lot!!
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Received on Wed Jan 01 2014 - 13:00:02 PST
