Objective and OverviewThis tutorial provides an overview of the CHARMM commands required to build and simulate either a DNA or RNA duplex in explicit solvent. In addition, an input file provides the appropriate CHARMM commands for converting RNA, which is the default nucleic acid in CHARMM, to DNA. Note, all remaining steps, including solvation, minimization, and simulation, are the same for both DNA and RNA. An image of a duplex is shown on the right |
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A nucleic acid duplex (PDB Identifer: 1RRR) is initially downloaded from the Protein Data Bank.
Then, the PDB coordinates are converted to CRD format acceptable to CHARMM. Topology and parameter files used for the calculations are the additive all-atom CHARMM Force Field Files which are located in the tutorial directory.
Once the initial CRD file is created for the RNA structure, it is then used in the CHARMM script file, helix_rna_gen.inp, from which a PSF file and new CRD file are obtained.
For the CHARMM force field, the RNA form of nucleic acids is the default.
Thus, for the building a DNA duplex structure, the CHARMM commands are almost the same as for the RNA duplex, but there is an additional step of removing the 2'OH moieties, as shown in the CHARMM script, helix_dna_gen.inp.
Small changes to the CHARMM scripts allow the use of a PDB file as input for the coordinates:
CHARMM CRD Input Coordinates open unit 20 read form name rr_1_noh.pdb.crd read coor card unit 20 |
PDB Input Coordinates rename segid a select segid rna1 end rename segid b select segid rna2 end open unit 20 read form name rr_1.pdb read coor pdb unit 20 resid rename segid rna1 a select segid a end rename segid rna2 b select segid b end |
For PDB file input, the segment names are renamed for each chain to match those in the rr_1.pdb file, and then changes them back so the segments have the same names in the later CHARMM scripts. |
The remainder of the CHARMM scripts involve equilibration of the system around the RNA followed by the production MD simulation. During equilbration, the coordinates of the DNA/RNA are harmonically constrained and a minimization is performed. This is followed by a NVT simulation to allow the solvent and ions to equilibrate around the nucleic acid. The final coordinates from the equilibration are used for the production simulation,
The production simulation involves an NPT simulation with long-range electrostatics treated via the Particle-Mesh Ewald method. Note, that the trajectory is run, such that a series of trajectory files, along with the associated restart are created. This allows the simulation to be readily restarted and facilitates handling of the files during analysis.
Two simple analysis CHARMM scripts to determine the RMS Differences as a function of time (rms.inp) and the base pairing energy as a function of time (bp_interactions.inp) are included in the analysis subdirectory.
Then, run the CHARMM script files in the analysis directory:
cd analysis charmm < rms.inp > rms.log charmm < bp_interactions.inp > bp_interactions.log