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Author Topic: Using find_pair  (Read 5815 times)

Offline jdap1989

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Using find_pair
« on: September 18, 2012, 07:39:13 pm »
Hello,

I've installed X3DNA in my Linux Ubuntu machine (the 32-bits version) and I tried to run one MD trajectory on pdb with find_pair, but I received this error message:
open_file <filename.pdb> failed: Value too large for defined data type.

I know the pdb is huge (more than 2 GB), but I could run it easily on my Mac.
Also, I tried to installed the 64-bits version (thinking that would fix it), but when I tried to compile it, I kept saying that the binary was not compatible.

What should I do?

Thanks,  :)

Johnny

Offline xiangjun

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Re: Using find_pair
« Reply #1 on: September 18, 2012, 09:52:28 pm »
Thanks for using 3DNA and for posting your question on the forum.

Which version of 3DNA are you using:, v1.5, v2.0 or v2.1beta? What's your Linux variant -- what's the output of running "uname -a"?

What do you mean specifically that you could run the huge 2GB+ pdb file easily on your Mac? Using "find_pair" or other programs?

This is the first time I meet such a question, so I have more questions to you before I could possibly provide a solution.

Xiang-Jun

Offline jdap1989

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Re: Using find_pair
« Reply #2 on: September 18, 2012, 11:08:34 pm »
Hi Xiang-Jun

Ok... The version I'm using is v2.1beta. I'm not exactly sure of the Linux variant, that only think I'm sure is Ubuntu :-/
The output of "uname -a" is

Linux ares 2.6.32-41-generic #91-Ubuntu SMP Wed Jun 13 11:44:43 UTC 2012 i686 GNU/Linux

I'm using "find_pair" to create the input files for "x3dna_ensemble".
In my mac I used this command to create the input files without a problem and in less than a second (that's what I mean with it ran easily). But I tried to do the same in my Linux computer, and the error message appeared.

Johnny

Offline xiangjun

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Re: Using find_pair
« Reply #3 on: September 18, 2012, 11:33:25 pm »
Hi Johnny,

Thanks for your follow-up; it certainly helps clarify the situation:

The output of "uname -a" means your Ubuntu is 32-bit -- google "ubuntu 32 bit or 64 bit how to tell" for details. This explains why the 3DNA 64-bits version "was not compatible" on your machine.

So if you insist on using Ubuntu instead of Mac OS X, a Ubuntu 64-bit version seems the way to go.

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.