Hi everybody,
I am looking for a simple command line tool to calculate symmetry-corrected RMSD. Does anyone know of any open-source available script/program?
I have tried g_rms from Gromacs, and the rmsd.py tool from here: https://github.com/rasbt/protein-science/tree/master/scripts-and-tools/rmsd
But neither corrects for molecule symmetry. The only script which I found to correct for molecule symmetry is rmsd.py from the Maestro suite (using renumber option), but it is not open-source.
Dear Rodrigo
I am not sure if this Bioperl modules corrects the symmetry, but I remember using it some years ago:
http://search.cpan.org/~rulix/Bio-PDB-Structure-0.02/lib/Bio/PDB/Structure.pm
Best
Prash
No, I do not mean structural alignment, I mean for example correctly assigning an RMSD of 0 to a 180 degree rotated aromatic ring, for example. An example of an algorithm which does this (known as Hungarian algorithm) is implemented in Glide and also in DOCK 6. This algorithm was developed by Kuhn and Munkres between 1955 and 1957.
In fact, this symmetry-corrected RMSD is normally used to correctly assess the results of docking, so no superimposition of ligands must be performed.
The paper describing the implementation in DOCK6:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3958141/
The rmsd.py script provided by Schrodinger in the free version of Maestro allows pairwise symmetry-corrected RMSD, but it is extremely slow for some reason.
http://www.schrodinger.com/scriptcenter/
I have now found an alternative, vrms by Verachem, which also offers free academic licenses, but I have yet to test it:
http://www.verachem.com/products/vrms/
CPPTRAJ in AMBERTOOLS15 can calculate this. The command is "symmrmsd" at Page 553 of the mannual. AMBERTOOLS is free.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Programming Languages
- Python