[gmx-users] Superimposing dissimilar structures

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 9 07:36:37 CET 2012

On 9/01/2012 4:53 PM, John Ladasky wrote:
> 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?

Doesn't trjconv -fit rot+trans prompt for a group for each structure for 
the superposition? If so, you should be able to construct an index file 
with groups like

[ normal ]

3 45 223

[ scrambled ]

451 97 345

and fit those.

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