Biowiki:Tutorials-rna

Software and example files can be downloaded here: http://biomol.bme.utexas.edu/~davbell/RNACG

Mapping to RACER coarse-grained coordinates starting from PDB crystal structure

Example: 1AL5

Example key file:

Parameters /home/user/RNA_CG.prm
DEBYE-HUCKEL  
openmp-threads 1
dielectric 25
debye-length 10
vdwtype           LJ-LP
#Canonical Hydrogen bonds
#G-C
CGHBOND  3  6  5  8  4  7   2.0  2.9  6.0
CGHBOND  6  5  3  4  7  8   2.0  2.9  6.0
#A-U
CGHBOND  3  4  9  8  6  7   2.0  2.9  6.0

Instructions

1. Download 1AL5 pdb structure: 1al5.pdb (also found in /home/RNACG/examples/1al5.pdb) and copy it to a directory with the key file and mapping scripts
2. Run ./mapping_atocg.py 1al5.pdb
3. Run Tinker's pdbxyz.x for 1al5.pdb.pdb ; output will be 1al5.pdb.xyz
4. Run ./xyz2cg_xyz.py 1al5.pdb.xyz
5. Copy 1al5.pdb.xyz.xyz to 1al5.xyz ; ready to simulate
6. Can run minimize.x, dynamic.x, anneal.x, etc.

Example: 2K7E

key file:

Parameters /home/user/RNA_CG.prm
DEBYE-HUCKEL  
openmp-threads 1
dielectric 25
debye-length 10
vdwtype           LJ-LP
#Canonical Hydrogen bonds
#G-C
CGHBOND  3  6  5  8  4  7   2.0  2.9  6.0
CGHBOND  6  5  3  4  7  8   2.0  2.9  6.0
#A-U
CGHBOND  3  4  9  8  6  7   2.0  2.9  6.0
#Noncanonical Hydrogen Bonds
#G-U
CGHBOND  3  6  5  8  6  7   2.0  2.9  6.0
CGHBOND  6  5  3  6  7  8   2.0  2.9  6.0
#G-A
CGHBOND  3  6  5  3  4  9   2.0  2.9  6.0
CGHBOND  6  5  3  4  9  3   2.0  2.9  6.0 

Instructions

1. Download 2K7E pdb structure: 2k7e.pdb (also found in /home/RNACG/examples/2k7e.pdb) and copy it to a directory with the key file and mapping scripts
2. Run ./mapping_atocg.py 2k7e.pdb
3. Run Tinker's pdbxyz.x for 2k7e.pdb.pdb ; output will be 2k7e.pdb.xyz
4. Run ./xyz2cg_xyz.py 2k7e.pdb.xyz
5. Copy 2k7e.pdb.xyz.xyz to 2k7e.xyz ; ready to simulate
6. Can run minimize.x, dynamic.x, anneal.x, etc.

Mapping to RACER coarse-grained coordinates starting from sequence

key file: (this portion only)

Parameters  /home/RNACG/amber99.prm

Instructions

1. Run Tinker's nucleic.xyz program to generate pdb structure from sequence using amber all-atom parameters (amber99.prm, included in RNACG/params). Only works with single strands and duplexes. If more than two strands or one helical region, must create individually and manually combine.

   nucleic.x -p amber99.prm

2. Run Tinker's xyzpdb.x program to convert xyz to pdb file

   xyzpdb.x -p amber99.prm filename.xyz

3. Output is all-atom pdb file; can follow tutorial above, Starting from PDB crystal structure.

Mapping to all-atom coordinates from RACER coarse-grained coordinates

Example 1DQF

key file:

Parameters  /home/RNACG/amber99.prm

Instructions

1. Copy 1dqf.xyz from /home/RNACG/examples/1dqf.xyz to a directory with the key file and mapping scripts
2. ./cg_xyz2aa_pdb.py 1dqf.xyz
3. Run Tinker's pdbxyz.x for 1dqf.xyz.aa.pdb ; output will be 1dqf.xyz.aa.xyz. %*
4. Run Tinker's minimize.x for 1dqf.xyz.aa.xyz ; output will be 1dqf.xyz.aa.xyz_2, the all-atom structure.+*
5. Can run superpose.x, dynamic.x, etc. with all-atom structure
6. To visualize, convert to pdb using Tinker's xyzpdb.x for 1dqf.xyz.aa.xyz_2 ; output will be 1dqf.xyz.aa.pdb_2
7. Move 1dqf.xyz.aa.pdb_2 to <filename>.pdb for visualization

%* Use at least Tinker6 or newer (Tinker7 is used for the CG model). It will print out two warnings of undefined dihedral angles for atoms 63 and 127; these warnings can be ignored as long as the xyz file is written and the next step works correctly.

+* If minimization fails, run minimize.x again on the 1dqf.xyz.aa.xyz_2 structure. The 1dqf.xyz.aa.xyz_3 structure will then be the all-atom structure.