Re: [AMBER] Combine trajectory files error

From: Steve Seibold <>
Date: Fri, 9 Jul 2010 08:32:45 -0400

Hi Daniel
I tried the script you suggested below. Ptraj recognized all sets and combined them successfully.

It appears the segmentation fault only comes by combining trajectory files and saving trajout file.

Is there something that can be done to fix this??

Thanks for your response.

Cheers, Steve

-----Original Message-----
From: Daniel Roe []
Sent: Thursday, July 08, 2010 10:35 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Combine trajectory files error

Hi Steve,

Sorry for the delay in replying.

The segmentation fault you report is apparently terminating ptraj before it has a chance to finish writing out all of the coordinate sets, which results in your "Could not predict frames" error.

Does the error occur if you do not attempt to combine the trajectories and calculate the rmsd directly, omitting the 'trajout' command? That is, if you were to do something like this:

trajin 1ps.mdcrd
trajin 1ps2.mdcrd
rms first out rmsd.dat

Do you still get the segfault?

On Fri, Jun 25, 2010 at 10:54 AM, Steve Seibold <> wrote:
> Hello AMBER
> I apologize for the being some what long. I just wanted it to be coherent.
> I have just serially compiled AMBER11 (with bug fixes) and its toolset1.4 (with bug fixes) as I wrote yesterday, and it did pass all its tests.
> I have run into a curious error that keeps showing up when using the ptraj package.
> Here is the protocol that consistently gives me an error:
> 1) I set up a 1.0 ps MD run and save a 1ps.mdcrd file. I then repeat this run to get a second 1 ps mdcrd file called 1ps2.mdcrd.
> 2) I then check each md trajectory file with checkcoords (using rdparm) and it counts 25 sets which is correct.
> 3) I then combine both md trajectories (1ps.mdcrd and 1ps2.mdcrd) into one, called combined.mdcrd using ptraj. During the process the print to the screen analysis shows that "checkcoords" is successful in recognizing the two 25 sets and says "Coordinate processing will occur on 50 frames". However, the last line printed to screen is "./ptraj: line 1: 25941 Segmentation fault ptraj file.prmtop"
> 4) Then when I checkcoords, again using rdparm, on the "combined.mdcrd" I get the error "Could not predict number of frames....etc".
> 5) I then ignore the error and use the "combined.mdcrd" to calculate the rms of the protein and this works fine except that I lose around 0.3 ps out of a total of 2ps...I am assuming this is because of the trajectory cut short when I combined...not sure.
> I am using AMBER11 for all except that my topology file which was constructed from AMBER8.
> AMBER11 is serially compiled, but I am waiting to check this problem out before I attempt a parallel compilation which is already out of my scope of efficiency .
> My trajectories are only a total of 1ps with each trajectory file. Could that be the problem? The files are just too small for ptraj to deal with?? I hesitate in doing longer serial runs...My protein is large and has explicit waters and so, it is time consuming.
> I did search the AMBER archives for this and found a developmental error, but it seemed to be a problem with compressed files. My files are not compressed.
> Thanks much for the help I have received,
> Steve
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
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Received on Fri Jul 09 2010 - 06:00:08 PDT
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