Creates a Karanicolas and Brooks coarse-grained protein model from a protein data bank file and a control file
citation for kb_cg model: (1) O’Brien, E. P.; Ziv, G.; Haran, G.; Brooks, B. R.; Thirumalai, D. Effects of Denaturants and Osmolytes on Proteins Are Accurately Predicted by the Molecular Transfer Model. Proc. Natl. Acad. Sci. U. S. A. 2008. https://doi.org/10.1073/pnas.0802113105.
- The pdb use HSE instead of HIS for histidine residues
- The pdb cannot be missing residues. If it is use:
[path-to-charmm-exe] < rebuild_solv_ions_definitive_v1.2.inp pdbin=[path-to-pbd-file-to-rebuild] label=[label-for-output-files] aatop=[path-to-top_all27_prot_na.rtf] aaprm=[path-to-par_all27_prot_na.prm]
- The pdb must also have the following form:
ATOM 1 N MET A 1 1.325 0.000 0.000 1.00 0.00
ATOM 2 HT1 MET A 1 1.746 0.686 0.658 1.00 0.00
ATOM 3 HT2 MET A 1 1.356 -0.949 0.423 1.00 0.00
ATOM 4 HT3 MET A 1 0.337 0.263 -0.189 1.00 0.00
ATOM 5 CA MET A 1 2.073 0.000 -1.245 1.00 0.00
ATOM 6 HA MET A 1 1.985 1.012 -1.640 1.00 0.00
ATOM 7 CB MET A 1 3.533 -0.363 -0.964 1.00 0.00
ATOM 8 HB1 MET A 1 3.676 -0.302 0.140 1.00 0.00
ATOM 9 HB2 MET A 1 3.719 -0.331 0.109 1.00 0.00
ATOM 10 CG MET A 1 4.484 0.597 -1.681 1.00 0.00
ATOM 11 HG1 MET A 1 4.877 0.130 -2.608 1.00 0.00
ATOM 12 HG2 MET A 1 4.857 0.137 -2.596 1.00 0.00
ATOM 13 SD MET A 1 5.850 1.016 -0.611 1.00 0.00
ATOM 14 CE MET A 1 5.083 2.280 0.389 1.00 0.00
ATOM 15 HE1 MET A 1 5.586 2.335 1.354 1.00 0.00
ATOM 16 HE2 MET A 1 5.163 3.242 -0.118 1.00 0.00
ATOM 17 HE3 MET A 1 4.032 2.036 0.541 1.00 0.00
ATOM 18 C MET A 1 1.481 -1.000 -2.241 1.00 0.00
ATOM 19 O MET A 1 2.212 -1.766 -2.866 1.00 0.00
If it does not you can use the following for conversion:
python convert_pdb_for_multimer_cg_v1.1.py [path-to-input-pdb] [path-to-output-pdb] [rebuild Yes:1 No:0] [path-to-seq_file]
NOTE: this conversion script is not perfect as there are many different forms a PDB can take depending on when and by what it was created. The script is simple enough that any beginner pythoner can modify it.
-The input PDB should contain a single chain. If you are doing multimer CGing you will need to use this conversion script on all chains in separate PDB files before CGing. -The [path-output-pdb] is a path to the output pdb minus the .pdb filetag as that will automatically be added -If you are rebuilding parts of a sequence or adding a mutation you must provide a file [path-to-seq_file] that has two columns
MET 1
VAL 2
ALA 3
. .
. .
. .
where the first column is the sequence of 3 letter amino acid codes and the second column is the resid in the PDB. If you resid does not start at 1 as you are CGing a subsection of a protein it will be rescaled to start from 1 as the rebuilding process in CHARMM requires this.
use:
perl create_cg_protein_model_v37.1.pl [path-to-control-file] [path-to-shared-files-folder]
see monomer_test/nbd1/input/nbd1_n1.1725_go.cntrl for an example control file and output
| cntrl file param | description |
|---|---|
| charmm | path to charmm executable hacked or modified with correct deby huckel electrostatics and double well angle pot |
| pdb | path to input pdb |
| nscal | scaling factor for the sidechain sidechain nonbonded interaction |
| pot | type of generic potential to use: bt, mj, kgs |
| bondlength_go | use a go model bondlength 0:no 1:yes |
| dihedral_go | use a go model dihedral potential 0:no 1:yes |
| casm | alpha-carbon side-chain model 0:no 1:yes |
| charges | include electrostatics 0:no 1:yes |
| angle_dw | include double well angle pot 0:no 1:yes |
| fnn | a multiplicative value which modifies the radius of the hard spheres used in the coarse-grain model |
| ca_name | name of model segments for alpha-carbon only CG model |
| sc_name | name of side-chains for alpha-carbon side-chain CG model |
| nbxmod | non-bonded local cutoff see https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/nbonds/ |
| heav_cut | cutoff for sidechain heavy atom contacts |
charmm = [path-to-charmm-exe]
pdb = [path-to-prepared-pdb]
nscal = 1.8
pot = bt
bondlength_go = 0
dihedral_go = 0
casm = 0
charges = 1
angle_dw = 1
fnn = 1
ca_name = A
sc_name = none
nbxmod = 4
heav_cut = 4.5
NOTE: this CG procedure requires the hacked version of charmm specific to our group. It also requires special perl and fortran scripts that are currently only available to our group. We are working to make these public in the near future.
Main outputs for input pdb:\
- [pdb-file-name]_ca.cor
- [pdb-file-name]_ca.psf
- [pdb-file-name]_ca.top
- [pdb-file-name]_[nscal]_[fnn]_go_[pot].prm
- [pdb-file-name]_ca.seq
- [pdb-file-name]_ca_mini.cor
NOTE: other other files are created during the CG procedure that are not necessary for running Molecular Dynamics
python ../../../parse_cg_prm.py -p [path-to-parameter-file] -t [path-to-topology-file]
- Each monomer of the n monomer multimer should have its own pdb
- The pdb use HSE instead of HIS for histidine residues
- The pdb cannot be missing residues. If it is use:
[path-to-charmm-exe] < rebuild_solv_ions_definitive_v1.2.inp pdbin=[path-to-pbd-file-to-rebuild] label=[label-for-output-files] aatop=[path-to-top_all27_prot_na.rtf] aaprm=[path-to-par_all27_prot_na.prm]
- The pdb must also have the following form:
ATOM 1 N MET A 1 1.325 0.000 0.000 1.00 0.00
ATOM 2 HT1 MET A 1 1.746 0.686 0.658 1.00 0.00
ATOM 3 HT2 MET A 1 1.356 -0.949 0.423 1.00 0.00
ATOM 4 HT3 MET A 1 0.337 0.263 -0.189 1.00 0.00
ATOM 5 CA MET A 1 2.073 0.000 -1.245 1.00 0.00
ATOM 6 HA MET A 1 1.985 1.012 -1.640 1.00 0.00
ATOM 7 CB MET A 1 3.533 -0.363 -0.964 1.00 0.00
ATOM 8 HB1 MET A 1 3.676 -0.302 0.140 1.00 0.00
ATOM 9 HB2 MET A 1 3.719 -0.331 0.109 1.00 0.00
ATOM 10 CG MET A 1 4.484 0.597 -1.681 1.00 0.00
ATOM 11 HG1 MET A 1 4.877 0.130 -2.608 1.00 0.00
ATOM 12 HG2 MET A 1 4.857 0.137 -2.596 1.00 0.00
ATOM 13 SD MET A 1 5.850 1.016 -0.611 1.00 0.00
ATOM 14 CE MET A 1 5.083 2.280 0.389 1.00 0.00
ATOM 15 HE1 MET A 1 5.586 2.335 1.354 1.00 0.00
ATOM 16 HE2 MET A 1 5.163 3.242 -0.118 1.00 0.00
ATOM 17 HE3 MET A 1 4.032 2.036 0.541 1.00 0.00
ATOM 18 C MET A 1 1.481 -1.000 -2.241 1.00 0.00
ATOM 19 O MET A 1 2.212 -1.766 -2.866 1.00 0.00
If it does not you can use the following for conversion:
python convert_pdb_for_multimer_cg_v1.1.py [path-to-input-pdb] [path-to-output-pdb] [segid]
NOTE: this conversion script is not perfect as there are many different forms a PDB can take depending on when and by what it was created. The script is simple enough that any beginner pythoner can modify it.
-The input PDB should contain a single chain. If you are doing multimer CGing you will need to use this conversion script on all chains in separate PDB files before CGing. -The [path-output-pdb] is a path to the output pdb minus the .pdb filetag as that will automatically be added -If you are rebuilding parts of a sequence or adding a mutation you must provide a file [path-to-seq_file] that has two columns
MET 1
VAL 2
ALA 3
. .
. .
. .
where the first column is the sequence of 3 letter amino acid codes and the second column is the resid in the PDB. If you resid does not start at 1 as you are CGing a subsection of a protein it will be rescaled to start from 1 as the rebuilding process in CHARMM requires this.
use:
perl create_cg_protein_model_v37.1.pl [path-to-control-file] [path-to-shared-files-folder]
see multimer_test/go_model.cntrl for an example control file and output
| cntrl file param | description |
|---|---|
| charmm | path to charmm executable hacked or modified with correct deby huckel electrostatics and double well angle pot |
| pdb | space separatetd paths to input pdbs 1 to n |
| nscal | scaling factor for the sidechain sidechain nonbonded interaction |
| pot | type of generic potential to use: bt, mj, kgs |
| bondlength_go | use a go model bondlength 0:no 1:yes |
| dihedral_go | use a go model dihedral potential 0:no 1:yes |
| casm | alpha-carbon side-chain model 0:no 1:yes |
| charges | include electrostatics 0:no 1:yes |
| angle_dw | include double well angle pot 0:no 1:yes |
| fnn | a multiplicative value which modifies the radius of the hard spheres used in the coarse-grain model |
| ca_name | name of model segments for alpha-carbon only CG model |
| sc_name | name of side-chains for alpha-carbon side-chain CG model |
| nbxmod | non-bonded local cutoff see https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/nbonds/ |
| heav_cut | cutoff for sidechain heavy atom contacts |
charmm = [path-to-charmm-exe]
pdb = [path-to-prepared-pdb1] [path-to-prepared-pdb2] ... [path-to-prepared-pdbn]
nscal = 1.8
pot = bt bt bt bt bt bt bt
bondlength_go = 0 0 0 0 0 0 0
dihedral_go = 0 0 0 0 0 0 0
casm = 0
charges = 1 1 1 1 1 1 1
angle_dw = 1 1 1 1 1 1 1
fnn = 1
ca_name = A B C D E F G
sc_name = none none none none none none none
nbxmod = 4
heav_cut = 4.5
NOTE: this CG procedure requires the hacked version of charmm specific to our group. It also requires special perl and fortran scripts that are currently only available to our group. We are working to make these public in the near future.
Main outputs for each of the n input pdbs:\
- [pdb-file-name]_ca.cor
- [pdb-file-name]_ca.psf
- [pdb-file-name]_ca.top
- [pdb-file-name]_[nscal]_[fnn]_go_[pot].prm
- [pdb-file-name]_ca.seq
- [pdb-file-name]_ca_mini.cor
NOTE: other other files are created during the CG procedure that are not necessary for running Molecular Dynamics
python ../../../parse_cg_prm.py -p [path-to-parameter-file] -t [path-to-topology-file]