[AMBER] cpptraj align using the same numbering

From: Martin Rosellen <martinrosellen.googlemail.com>
Date: Wed, 16 Jun 2021 13:09:09 +0200

Dear Amber community,

I run a simulation of a hexamer and want to calculate RMSD values of hairpins found in each monomer. For that I want to align the protein body. When I aligned the first two frames in Chimera, I found out that aligning does not necessarily align monomer 1 with monomer 1. Instead it happened that the hexamer got rotated and monomer 1 was aligned with monomer 3 and so forth, which flaws the calculations of RMSD values. Is such a rotation an issue with ‘align’ in cpptraj? From what I have seen so far it seems to be not an issue but I wanted to be sure since for the best fit it might be necessary to rotate the hexamer.

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Received on Wed Jun 16 2021 - 04:30:02 PDT
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