Author: Rhiju Das

Dec. 2014 by Rhiju Das (rhiju [at]

Developed in summer 2012, Das Lab hackathon -- Kyle Beauchamp, Fang-Chieh Chou, Rhiju Das, Parin Sripakdeevong. Extended to include phosphate by Rhiju Das in Dec. 2014.

Scan methyl probe in base plane

Scan xy

Scan methyl probe 4.0 Å displaced from base plane

Scan xy, displaced by 4.0 Å


We wanted to compare potentials of mean force of various atoms like a single methyl probe, water, adenosine, etc. around a fixed adenosine to explicit molecular dynamics solutions.

Code and Demo

The code is in


with lots of helper functions in


Demo files are in




Application purpose

Make tables of interaction energies between an adenosine nucleobase and, say, a simple carbon atom or phosphate as a probe.


To sample a 'carbon' probe atom:

 nucleobase_sample_around   [-s a_RNA.pdb]

To sample a water (sampling all possible orientations and outputting Boltzmann summed free energies)

 nucleobase_sample_around   [-s a_RNA.pdb]  -sample_water  [ -extra_res /path/to/rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/water/TP3.params ]

To sample a nucleobase

 nucleobase_sample_around   [-s a_RNA.pdb]  -sample_another_nucleobase   -copy_nucleobase_nucleobase_file double_A_ready_set.pdb

To sample an nucleobase, reading in a starting nucleobase-nucleobase pairing conformation.

 nucleobase_sample_around   [-s a_RNA.pdb]  -sample_another_nucleobase   -copy_nucleobase_nucleobase_file double_A_ready_set.pdb

Can now sample phosphates with the flags

 nucleobase_sample_around -sample_phosphate [-center_on_OP2]

The phosphate center is on the phosphorus atom, unless user specifies -center_on_OP2 . Note that due to some silliness in available variant types and the desire to use a phosphate from an actual nucleotide residue_type, the probe phosphate also has a floating C1'.

Recently added option

 -nucleobase g [or a,c,u]

which will use something other than adenosine as the central nucleotide to sample around


The plotting script is available in Rosetta/tools/rna_tools/pdb_util/ score_xy_0.table score_xy_0.png score_xy_1.5.table score_xy_1.5.png score_xy_3.table score_xy_3.png score_xy_4.table score_xy_4.png

Additional Information

The previous hackathon results are summarized in the following slides

See Also