Author: Rhiju Das

Dec. 2014 by Rhiju Das (rhiju [at] stanford.edu).

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

Purpose

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

apps/public/rna_util/nucleobase_sample_around.cc

with lots of helper functions in

protocols/toolbox/sample_around/util.cc

Demo files are in

Rosetta/demos/public/nucleobase_sample_around

References

Unpublished.

Application purpose

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

Modes

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

Plotting

The plotting script is available in Rosetta/tools/rna_tools/pdb_util/plot_contour.py

plot_contour.py score_xy_0.table score_xy_0.png
plot_contour.py score_xy_1.5.table score_xy_1.5.png
plot_contour.py score_xy_3.table score_xy_3.png
plot_contour.py score_xy_4.table score_xy_4.png

Additional Information

The previous hackathon results are summarized in the following slides https://drive.google.com/file/d/0By0BpYZBGuK-R2dhcEpKN0E4d28/view?usp=sharing

Sample around nucleobase