AMBER Archive (2008)

Subject: RE: AMBER: Trajectory in "Sietraj"

From: Purisima, Enrico (
Date: Tue Jun 03 2008 - 09:39:49 CDT

Dear Alfredo,

This error can arise from very large systems or for long extended unfolded proteins. How large is your system? You can try editing the sietraj.tcl file in the apps/sietraj directory. Change the value 200000 in the line

set MarTet_TMP_SIZE 200000

to 300000 or some larger number.

The error can also be a side-effect of a mismatch between the prmtop and trajectory file. If you wish, you can send me a copy of your prmtop file and a few frames of your trajectory file and I can look into the error. (If these are big files, you can send them offline to



-----Original Message-----
From: [] On Behalf Of Alfredo Quevedo
Sent: Tuesday, June 03, 2008 10:09 AM
Subject: Re: AMBER: Trajectory in "Sietraj"

Dear Enrico: the error message is:

(MarTetSurf: : Out3) MarTet_TMP_SIZE exceeded.



----- Original Message -----
From: "Purisima, Enrico" <>
To: <>
Sent: Tuesday, June 03, 2008 10:55 AM
Subject: RE: AMBER: Trajectory in "Sietraj"

> Dear Alfredo,
> The trajectory used is an Amber trajectory with water molecules
> stripped
> out and generated with the nobox option. The suffix .trj was an
> arbitrarily chosen suffix in the examples and not meant to imply Gromacs
> files. Could you post the error messages? A common cause of errors is
> missing atom types.
> Regards,
> Enrico
> ---------
> Enrico O. Purisima
> Biotechnology Research Institute
> National Research Council Canada
> -----Original Message-----
> From: [] On
> Behalf
> Of Alfredo Quevedo
> Sent: Tuesday, June 03, 2008 9:35 AM
> To:
> Subject: AMBER: Trajectory in "Sietraj"
> Dear Amber users. I have recently seen the link of the "Sietraj"
> application in Amberīs homepage, and found it ver interesting. I
> downloaded it and run the examples with everything running ok. I tried to
> apply this package to analyze my trajectories generated with Amber8 and
> found some errors with the calculation stoped. Searching the source of the
> problem, I find out that the examples of Sietraj are based on a .trj
> trajectory (I think that is Gromacs), so here comes my question: Has
> anyone tryed this software using an Amber trajectory? Otherwise, is there
> a way to convert the .mdcrd files into a .trj file?
> Thanks in advance for the help,
> Best regards
> Alfredo Quevedo
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