[AMBER] shape of a peptide array

From: Fabian gmail <fabian.glaser.gmail.com>
Date: Mon, 4 Jan 2016 13:54:34 +0200


What is the best way to calculate the change in SHAPE of a protein (in my specific case an array of peptides) during simulation?
RMSD helps and also Rg but they don’t give me exactly the change in shape….

Is there a way to do that effectively in cpptraj?

I saw something similar in MDanalysis, but I wouldn’t like to start dealing with python issues….

Best and and thanks in advance,


Dr. Fabian Glaser
Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il
Tel: +972 4 8293701

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Received on Mon Jan 04 2016 - 04:00:03 PST
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