The scripts and input files that accompany this demo can be found in the demos/public directory of the Rosetta weekly releases.

KEYWORDS: NUCLEIC_ACIDS UTILITIES

Author

Rhiju Das, rhiju@stanford.edu

Edited by Parisa Hosseinzadeh (parisah@uw.edu) during XRW documentation 2016 to enable automatic testing of demos.

Brief Description

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

Abstract

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.

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.

Running

To sample a 'carbon' probe atom: 

 $> $ROSETTA3/bin/nucleobase_sample_around.default.linuxgccrelease  -s rosetta_inputs/a_RNA.pdb
where $ROSETTA3=path-to-Rosetta/main/source

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

 $> $ROSETTA3/bin/nucleobase_sample_around.default.linuxgccrelease  -s rosetta_inputs/a_RNA.pdb  -sample_water
To sample a nucleobase 
 $> $ROSETTA3/bin/nucleobase_sample_around.default.linuxgccrelease  -s rosetta_inputs/a_RNA.pdb  -sample_another_nucleobase   -copy_nucleobase_nucleobase_file rosetta_inputs/double_A_ready_set.pdb
To sample an nucleobase, reading in a starting nucleobase-nucleobase pairing conformation. 
 $> $ROSETTA3/bin/nucleobase_sample_around.default.linuxgccrelease  -s rosetta_inputs/a_RNA.pdb  -sample_another_nucleobase   -copy_nucleobase_nucleobase_file rosetta_inputs/double_A_ready_set.pdb
Can now sample phosphates with the flags 
 $> $ROSETTA3/bin/nucleobase_sample_around.default.linuxgccrelease -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 Results

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