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

From: Jonathan Saboury <>
Date: Wed, 1 Jan 2014 12:51:57 -0800

> Can you provide more information? What makes you think that sqm ran out
> 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

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
Received on Wed Jan 01 2014 - 13:00:02 PST
Custom Search