[AMBER] Distance calculation and distance matrix giving discrepant results

From: Jonathan Huihui <Jonathan.Huihui.du.edu>
Date: Thu, 2 May 2019 16:25:55 +0000


I have been getting different results for the distances between C-alpha atoms when I use the "distance" command and the "matrix dist" commands, and I'm not sure which set of values to believe.

Here is what I'm using as commands (trying to see the end-to-end distance):

>>distance Ree :1.CA :64.CA out Ree.dat
>>matrix out Rij.dat name Rij byres .CA dist

However, when I use "noimage" in the distance command, it returns a value that agrees with the matrix command.
Furthermore, when I output the entire trajectory as a set of PDBs, and run separate analysis on those with my own code, it agrees with the matrix command results.

I am running these analyses on trajectories that have been stripped of water and ions using these commands:
>>strip :WAT,Cl-,Na+
>>rms first .CA,C,N
>>trajout output.mdcrd trajectory

I am thinking that the trajectory already being "autoimaged" is what is causing this?
Is there any additional information that is required?

Thank you,

Jonathan Huihui

Graduate Student, University of Denver

Department of Physics & Astronomy

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Received on Thu May 02 2019 - 09:30:02 PDT
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