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small_z Offline OP
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I have run a trajectory for 1 ns, and I want to obtain the average structure of protein in the trajectory.

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Have a look at the examples in the Script Archive forum, they can help you get started with basic tasks.
The command you need is "COOR DYNA" (corman.info):
read rtf card name ...
read para card name ..
read psf card name ..
read coor card name starting_coordinate_file
coor copy comp
open file unit 101 name name_of_your_trajectory_file
coor dyna orient firstunit 101 nunit 1 select segi segment_id_of_your_protein end
write coor card name average.crd select segi segment_id_of_your_protein end
* average coordinates over 1 ns
*


Lennart Nilsson
Karolinska Institutet
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Keep in mind that an average structure may be highly non-physical, esp. internal coordinates such as bond angles and dihedrals. I often choose to obtain a real coordinate set that is closest to the average in terms of RMS difference for Calphas of conserved structural elements such as helices, sheets, and turns.


Rick Venable
computational chemist

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Totally agree with Rick, who as usual focuses on science. This is something you should discuss at depth with you supervisor. One may also add that:
1/ 1 nanosecond may be too short
2/ It may be more relevant to describe the trajectory either in terms of a real structure close to the average as Rick suggests, or in terms of representative members of the main clusters obtained from a clustering analysis.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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