AMBER Archive (2009)

Subject: Re: [AMBER] problem about trajectory analysis

From: Thomas Cheatham III (
Date: Wed Feb 25 2009 - 18:57:49 CST

> Are there
> any Amber users who perform analysis apart from Amber ptraj ? I want
> to extact the information from mdcrd and rst files with any order and
> use the trajectory information with other Analysis software .
> But I have a limited information about shell scripting. In this
> sense, I'm waiting for the people's help who have enough experience
> on this topic.

To move forward-- beyond simply understanding the formats as previously
advised at it is imperative that you
learn more about shell scripting or a more rich language like Perl,
Python, F90 or C, or some other language. Otherwise, even if people send
you partial scripts or solutions, you will still likely be stuck.

If you were my graduate student, I would advise you to look at "Learning
Perl" from the O'Reily series (or some of many Perl tutorials on the WWW)
and try to write a Perl script that reads in the AMBER files, does
whatever conversion is necessary, and then calls the other analysis codes.
Perl is really good at processing text files and also can spawn separate
programs; it is relatively easy to learn and highly portable.

If you simply need a different format for the coordinates, the Babel
programs ( can do many conversions; although you seem
content on avoiding ptraj, ptraj can extract frames of interest and output
into PDB... Babel can do many conversions.

Good luck. --tec3

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