[gmx-users] Superimposing dissimilar structures
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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