[gmx-users] Superimposing dissimilar structures

John Ladasky blind.watchmaker at yahoo.com
Mon Jan 9 06:53:49 CET 2012

Hello everyone,

I've used the rot+trans option in GROMACS trjconv to superimpose groups of atoms within a single molecular dynamics simulation.  I am now interested in modeling a protein, and a rather thoroughly scrambled circular permutation of that same protein.  I want to construct a superimposition which optimizes the alignment of selected residues within the two structures.  But unlike in a standard trjconv superimposition, I will be trying to align atoms in one structure which correspond to atoms with different numbers in the other structure.  So the idea of groups as numbered atoms, as conventionally defined in a GROMACS .ndx file, would not seem to apply here.

Is this a practical task within GROMACS, or should I be looking elsewhere for the tool to accomplish the job?

Many thanks for your advice.
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