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2022-05-12T14:39:37Z

Created page with " <big>Software and example files can be downloaded here: http://biomol.bme.utexas.edu/~davbell/RNACG</big> = 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..."

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

= 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

# 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
# Run ./mapping_atocg.py 1al5.pdb
# Run Tinker's pdbxyz.x for 1al5.pdb.pdb ; output will be 1al5.pdb.xyz
# Run ./xyz2cg_xyz.py 1al5.pdb.xyz
# Copy 1al5.pdb.xyz.xyz to 1al5.xyz ; ready to simulate
# 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

# 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
# Run ./mapping_atocg.py 2k7e.pdb
# Run Tinker's pdbxyz.x for 2k7e.pdb.pdb ; output will be 2k7e.pdb.xyz
# Run ./xyz2cg_xyz.py 2k7e.pdb.xyz
# Copy 2k7e.pdb.xyz.xyz to 2k7e.xyz ; ready to simulate
# 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

# 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
# Run Tinker's xyzpdb.x program to convert xyz to pdb file
#: xyzpdb.x -p amber99.prm filename.xyz
# 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

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

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