Re: [AMBER] SQM seems to run out of memory?

From: FyD <>
Date: Thu, 02 Jan 2014 09:22:21 +0100

Dear Jonathan,

> Here is the .pdb:

I think you should split this molecule into elementary building blocks.

See two examples in R.E.DD.B. by E. Vanquelef

You could use R.E.D. Server/Ante_R.E.D. 2.0 and R.E.D. IV or better
R.E.D. Server Dev./R.E.D. Python at

regards, Francois

>> 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 file (or input pdb file). Without more
>> information, people on the list cannot be of much help here.
>> ...dac
> Here is the .pdb:
> 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?

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Received on Thu Jan 02 2014 - 00:30:03 PST
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