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.
Mark
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