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How to get the average structure of protein in a trajectory
#38283 06/03/21 03:56 AM
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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.

Re: How to get the average structure of protein in a trajectory
small_z #38284 06/03/21 07:03 AM
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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
Stockholm, Sweden
Re: How to get the average structure of protein in a trajectory
small_z #38285 06/03/21 04:33 PM
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rmv Online Content
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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

Re: How to get the average structure of protein in a trajectory
small_z #38286 06/03/21 05:49 PM
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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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