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

From: Alan <>
Date: Wed, 1 Jan 2014 22:21:15 +0100

Hi, it's a quite big system for SQM, but it's possible, but it depends on
how much memory you do have available in your computer/cluster. And it can
a long long time to execute.

About dividing your system, you can divide it in 3 parts, where the 3rd one
would encompass the border atom and its neighbourhood involved in parts 1
and 2. And you may need to add atoms to the fragments to avoid open


On 1 January 2014 21:51, Jonathan Saboury <> wrote:

> > 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?
> Thanks a lot!!
> _______________________________________________
> AMBER mailing list

Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Received on Wed Jan 01 2014 - 13:30:03 PST
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