I had a similar problem. ptraj would not process the file. I tried splitting the file but got weird results. I have no idea why this did not work. I then gzip'd it and fed it to ptraj and it was processed, no complaints. Maybe it'll work for you, too.
Pete
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Jason Swails [jason.swails.gmail.com]
Sent: Wednesday, March 17, 2010 12:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Large FIle
Just another thought -- if you're not using AmberTools 1.3, I would
suggest building it since there are significant upgrades to file I/O
done for ptraj. Using AT 1.3, did you try doing something like this:
trajin big.mdcrd 1 [half frames] 1
trajout smaller_1.mdcrd
-----------------------------------------------------------------
trajin big.mdcrd [half frames] [num frames] 1
trajout smaller_2.mdcrd
(The above is two separate files with two separate ptraj runs.) The
ptraj in AT 1.3 will not read the entire file, but only the portion
loaded by the trajin statements. This could circumvent your error (no
guarantees...).
Good luck!
Jason
On Wed, Mar 17, 2010 at 11:54 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> I did an MD simulation and had my ntwx parameter set too small. As a
> result, the *.mdcrd file is very large, and ptraj will not open it. Is
> there a way to split the *.mdcrd file into two equal but smaller files?
>
>
>
> John
>
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> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Mar 17 2010 - 10:00:03 PDT
