Dear Jonathan,
> Here is the .pdb: http://pastebin.com/raw.php?i=bP2Dfd3Z
I think you should split this molecule into elementary building blocks.
See two examples in R.E.DD.B. by E. Vanquelef
http://q4md-forcefieldtools.org/REDDB/projects/F-87/
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
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 q4md-forcefieldtools.org
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 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?
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Received on Thu Jan 02 2014 - 00:30:03 PST
