Package to generate Coarse-Grained Structure (.gro/.pdb) and Topology (.top/.xml) for using Augmented Structure Based Models MD Simulations on GROMACS and OpenSMOG (OpenMM based)
1. CA-SBM (Clementi et al., 2000. https://doi.org/10.1006/jmbi.2000.3693)
$ python submit.py --clementi2000 --aa_pdb [All-atom .pdb file]
2. CA-CB SOP-SC model (Maity and Reddy, 2016. https://pubs.acs.org/doi/abs/10.1021/jacs.5b11300)
$ python submit.py --reddy2016 --aa_pdb [All-atom .pdb file]
$ python submit.py --reddy2016 --cg_pdb [Coarse-grained .pdb file]
3. CA-CB SOP-SC-IDP model (Baidya and Reddy, 2022. https://doi.org/10.1021/acs.jpclett.2c01972)
$ python submit.py --aa_pdb/--cg__pdb [template AA/CG .pdb file]
$ python submit.py --baidya2022 --idp_seq [IDP sequence .fa file]
4. CA-CB SOP-SC-MULTI model (Baratam and Srivastava, 2024.https://doi.org/10.1021/acs.jctc.4c00579)
$ python submit.py --baratam2024 --idp_seq [IDP sequence .fa file (see models/baratam2024/example.fa)]
5. CA-CB Protein+RNA/DNA model with DH-electrostatics (Pal and Levy, 2019. https://doi.org/10.1371/journal.pcbi.1006768)
$ python submit.py --pal2019 --aa_pdb [protein All-atom .pdb file] --custom_nuc [RNA/DNA all-atom .pdb file]
$ python submit.py --pal2019 --aa_pdn [protein AA .pdb] [RNA/DNA AA .pdb]
6. For every model, predefined parameters can be customized. For example, for changing angle force constant in Pal 2019 model
$ python submit.py --pal2019 --aa_pdb [protein All-atom .pdb file] --Ka_prot 80
$ python submit.py --help
-h, --help show this help message and exit
NOTE 1: Based on the information available to us, we have implemented the models listed below in accordance with their respective publications. If any contributors to the development of these models identify any bugs, errors, or incorrect parameters, we kindly request that they raise an issue on the GitHub page.
--clementi2000, -clementi2000, --calpha_go2000, -calpha_go2000
Clementi et. al. 2000 CA-only model.
10.1006/jmbi.2000.3693
--afsar2008, -afsar2008, --chan2008, -chan2008
Zarrine-Afsar et. al. 2008 CA-only + hydrophobic model with.
10.1073/pnas.0801874105
--azia2009, -azia2009, --levy2009, -levy2009
Azia 2009 CB-CA + Debye-Huckel model.
10.1016/j.jmb.2009.08.010
--pal2019, -pal2019, --levy2019, -levy2019
Pal & Levy 2019 Protein CB-CA & RNA/DNA P-S-B model.
10.1371/journal.pcbi.1006768
--reddy2016, -reddy2016, --maity2016, -maity2016, --sopsc2016, -sopsc2016
Maity & Reddy 2016 SOP-SC CA-CB.
10.1021/jacs.5b11300
--denesyuk2013, -denesyuk2013, --rna_tis2013, -rna_tis2013 [WIP]
Denesyuk & Thirumalai 2013 Three Interaction Site TIS
P-S-B model. 10.1021/jp401087x
--chakraborty2018, -chakraborty2018, --dna_tis2018, -dna_tis2018 [WIP]
Chakraborty & Thirumalai 2018 Three Interaction Site
TIS P-S-B model. 10.1021/acs.jctc.8b00091
--baul2019, -baul2019, --sop_idp2019, -sop_idp2019
Baul et. al. 2019 SOP-SC-IDP CA-CB.
10.1021/acs.jpcb.9b02575
--baidya2022, -baidya2022, --sop_idp2022, -sop_idp2022
Baidya & Reddy 2022 SOP-SC-IDP CA-CB.
10.1021/acs.jpclett.2c01972
--baratam2024, -baratam2024, --sop_multi, -sop_multi
Baratam & Srivastava 2024 SOP-MULTI CA-CB.
10.1021/acs.jctc.4c00579
--sop_idr, -sop_idr Reddy-Thirumalai(SOPSC) + Baidya-Reddy(SOPIDP) hybrid
CA-CB
--banerjee2023, -banerjee2023, --selfpeptide, -selfpeptide [WIP]
Banerjee & Gosavi 2023 Self-Peptide model.
10.1021/acs.jpcb.2c05917
--virusassembly, -virusassembly, --capsid, -capsid [TEST]
Preset for structure based virus assembly (inter-
Symmetrized)
--dlprakash, -dlprakash, --duplexpair, -duplexpair [TEST]
Codon pairs (duplex based weight) for Pal2019
--aa_pdb AA_PDB [AA_PDB ...], -aa_pdb AA_PDB [AA_PDB ...]
User input all-atom pdbfile/gro/mmCIF e.g. 1qys.pdb
--cg_pdb CG_PDB [CG_PDB ...], -cg_pdb CG_PDB [CG_PDB ...]
User input coarse grained pdbfile
--idp_seq IDP_SEQ, -idp_seq IDP_SEQ
User input sequence fasta file for building/extracting
IDRs/segments etc.
--nmol NMOL [NMOL ...], -nmol NMOL [NMOL ...]
Include nmol number of molecules in the topology. List
of integers. Defatul1 1 per input pdbfile
--gen_cg, -gen_cg Only Generate CG structure without generating topology
.top/.xml files
--outtop OUTTOP, -outtop OUTTOP
Gromacs topology file output name (tool adds prefix
nucl_ and prot_ for independednt files). Default:
gromacs.top
--outgro OUTGRO, -outgro OUTGRO
Name for output .gro file.(tool adds prefix nucl_ and
prot_ for independednt files). Default: gromacs.gro
--box BOX, -box BOX Width of the cubic simulation box. Default: 500.0 Å. Use 0 for no box.
--voxel VOXEL, -voxel VOXEL, --box_cell VOXEL, -box_cell VOXEL
Width of the minimal cubic volume unit, used to fill the simulation box.
Default: 1.618 Å
--outxml OUTXML, -outxml OUTXML
Name for output .xml (openSMOG) file.(tool adds prefix
nucl_ and prot_ for independednt files). Default:
opensmog.xml (and opensmog.top)
--opensmog, -opensmog
Generate files ,xml and .top files for openSMOG.
Default: False
--dihed2xml, -dihed2xml
Write torsions to opensmog xml. Adds conditon for angle->n*pi. Only supported for
OpensMOGmod:https://github.com/sglabncbs/OpenSMOGmod. Default: False
--prot_cg PROT_CG, -prot_cg PROT_CG
Level of Amino-acid coarse-graining 1 for CA-only, 2
for CA+CB. Dafault: 2 (CA+CB)
--nucl_cg NUCL_CG, -nucl_cg NUCL_CG
Level of Amino-acid coarse-graining 1 for P-only, 3
for P-S-B, 5 for P-S-3B. Dafault: 3 (P-S-B)
--CA_rad CA_RAD, -CA_rad CA_RAD
User defined radius (0.5*excl-volume-rad) for C-alpha
(same for all beads) in Angstrom. Default: 1.9 Å
--CA_com, -CA_com Place C-alpha at COM of backbone. Default: False
--CB_rad CB_RAD, -CB_rad CB_RAD
User defined radius (0.5*excl-volume-rad) for C-beta
(same for all beads) in Angstrom. Default: 1.5 Å
--cg_radii, -cg_radii
User defined CG-bead radii from radii.dat
(atype radius-in-Angsrtom). Default: False
--CB_com, -CB_com Put C-beta at side-chain COM. Default: False
--CB_far, -CB_far Place C-beta on farthest non-hydrogen atom. Default:
False
--CB_chiral, -CB_chiral
Improper dihedral for CB sidechain chirality
(CAi-1:CAi+1:CAi:CBi). Default: False
--CB_gly, --CB_GLY, -CB_gly, -CB_GLY
Add C-beta for glycine (pdb-file must have H-atoms).
Default: Flase
--P_rad P_RAD, -P_rad P_RAD
User defined radius for Backbone Phosphate bead.
Default= 1.9 Å
--S_rad S_RAD, -S_rad S_RAD
User defined radius for Backbone Sugar bead. Default=
1.9 Å
--Bpu_rad BPU_RAD, -Bpu_rad BPU_RAD
User defined radius for N-Base Purine bead.
Default=1.5 Å
--Bpy_rad BPY_RAD, -Bpy_rad BPY_RAD
User defined radius for N-Base Pyrimidine bead.
Default=1.5 Å
--Bpu_pos BPU_POS, -Bpu_pos BPU_POS
Put input atom of Purine
[N1,C2,H2-N2,N3,C4,C5,C6,O6-N6,N7,C8,N9,COM] as
position of B. Default=COM(Center_of_Mass)
--Bpy_pos BPY_POS, -Bpy_pos BPY_POS
Put input atom of Pyrimidine
[N1,C2,O2,N3,C4,O4-N4,C5,C6,COM] as position of B.
Default=COM(Center_of_Mass)
--S_pos S_POS, -S_pos S_POS
Put input atom of Sugar
[C1',C2',C3',C4',C5',H2'-O2',O3',O4',O5',COM] as
position of S. Default=COM(Center_of_Mass)
--P_pos P_POS, -P_pos P_POS
Put input atom of Phosphate [P,OP1,OP2,O5',COM] group
as position of P. Default=COM(Center_of_Mass)
--Kb_prot KB_PROT, -Kb_prot KB_PROT, --Kb KB_PROT, -Kb KB_PROT
User defined force constant K_bond for Proteins.
Default: 200.0 ε/Å^2 (ε = 1KJ/mol)
--Ka_prot KA_PROT, -Ka_prot KA_PROT, --Ka KA_PROT, -Ka KA_PROT
User defined force constant K_angle for Proteins.
Default: 40.0 ε/rad^2 (ε = 1KJ/mol)
--Kd_bb_prot KD_BB_PROT, -Kd_bb_prot KD_BB_PROT, --Kd KD_BB_PROT, -Kd KD_BB_PROT
User defined force constant K_dihedral for Proteins.
Default: 1.0 ε (ε = 1KJ/mol)
--Kd_sc_prot KD_SC_PROT, -Kd_sc_prot KD_SC_PROT, --Kd_chiral KD_SC_PROT, -Kd_chiral KD_SC_PROT
User defined force constant K_dihedral for Proteins.
Default: Use Ka_prot value
--mulfac_prot MULFAC_PROT, -mulfac_prot MULFAC_PROT
User defined Multiplicity scaling factor of
K_dihedral/mulfac_prot for Proteins. Default: 2
--Kr_prot KR_PROT, -Kr_prot KR_PROT
Krepulsion. Default=1.0 ε
--uniqtype, -uniqtype
Each atom has unique atom type (only use for large
systems)
--bfunc BFUNC, -bfunc BFUNC
Bond function 1: harnomic. Default: 1 (Harmonic)
--Kb_nucl KB_NUCL, -Kb_nucl KB_NUCL, --nKb KB_NUCL, -nKb KB_NUCL
User defined force constant K_bond for RNA/DNA.
Default: 200.0 ε/Å^2 (ε = 1KJ/mol)
--Ka_nucl KA_NUCL, -Ka_nucl KA_NUCL, --nKa KA_NUCL, -nKa KA_NUCL
User defined force constant K_angle for RNA/DNA.
Default: 40.0 ε/rad^2 (ε = 1KJ/mol)
--Kd_sc_nucl KD_SC_NUCL, -Kd_sc_nucl KD_SC_NUCL, --nKd KD_SC_NUCL, -nKd KD_SC_NUCL
User defined force constant K_dihedral for Bi-Si-
Si+1-Bi+1. Default: 0.5 ε (ε = 1KJ/mol)
--Kd_bb_nucl KD_BB_NUCL, -Kd_bb_nucl KD_BB_NUCL, --P_nKd KD_BB_NUCL, -P_nKd KD_BB_NUCL
User defined force constant K_dihedral for Backbone
Pi-Pi+1-Pi+2-Pi+3. Default: 0.7 ε (ε = 1KJ/mol)
--P_stretch P_STRETCH, -P_stretch P_STRETCH
Stretch the backbone dihedral to 180 degrees.
Default=Use native backbone dihedral
--mulfac_nucl MULFAC_NUCL, -mulfac_nucl MULFAC_NUCL
User defined Multiplicity scale factor of K_dihedral
for Nucleic Acids. Default: 1
--Kr_nucl KR_NUCL, -Kr_nucl KR_NUCL
Krepulsion. Default: 1.0 ε
--cutoff CUTOFF, -cutoff CUTOFF
User defined Cut-off (in Angstrom) for contact-map
generation. Default: 4.5 Å (for all-atom) or 8.0 Å
(for coarse-grianed)
--cutofftype CUTOFFTYPE, -cutofftype CUTOFFTYPE
-1 No map, 0 use -cmap file, 1 all-atom mapped to CG,
2: coarse-grain . Default: 1
--W_cont, -W_cont Weight (and normalize) CG contacts based on all atom
contact pairs
--cmap CMAP [CMAP ...], -cmap CMAP [CMAP ...]
User defined cmap in format chain1 atom1 chain2 atom2
weight(opt) distance(opt)
--scaling SCALING, -scaling SCALING
User defined scaling for mapping to all-atom contact-
map.
--contfunc CONTFUNC, -contfunc CONTFUNC
1: LJ C6-C12, 2 LJ C10-C12, 3 LJ C12-C18, 6 Gauss +
excl, 7 Multi Gauss . Default: 2
--cutoff_p CUTOFF_P, -cutoff_p CUTOFF_P
User defined Cut-off (in Angstrom) for Protein
contact-map generation. Default: 4.5 Å (for all-atom)
or 8.0 Å (for coarse-grianed)
--cutofftype_p CUTOFFTYPE_P, -cutofftype_p CUTOFFTYPE_P
For Proteins: -1 No map, 0 use -cmap file, 1 all-atom
mapped to CG, 2: coarse-grain . Default: 1
--W_cont_p, -W_cont_p
Weight (and normalize) Protein CG contacts based on
all atom contacts
--cmap_p CMAP_P [CMAP_P ...], -cmap_p CMAP_P [CMAP_P ...]
User defined Protein cmap in format chain1 atom1
chain2 atom2 weight(opt) distance(opt)
--scaling_p SCALING_P, -scaling_p SCALING_P
User defined scaling for mapping to all-atom contact-
map.
--contfunc_p CONTFUNC_P, -contfunc_p CONTFUNC_P
Proteins. 1: LJ C6-C12, 2 LJ C10-C12, 3 LJ C12-C18, 6
Gauss + excl, 7 Multi Gauss . Default: 2
--cutoff_n CUTOFF_N, -cutoff_n CUTOFF_N
User defined Cut-off (in Angstrom) for RNA/DNA
contact-map generation. Default. Default: 4.5 Å (for
all-atom) or 8.0 Å (for coarse-grianed)
--cutofftype_n CUTOFFTYPE_N, -cutofftype_n CUTOFFTYPE_N
For RNA/DNA. -1 No map, 0 use -cmap file, 1 all-atom
mapped to CG, 2: coarse-grain . Default: 1
--W_cont_n, -W_cont_n
Weight (and normalize) RNA/DNA CG contacts based on
all atom contacts
--cmap_n CMAP_N [CMAP_N ...], -cmap_n CMAP_N [CMAP_N ...]
User defined RNA/DNA cmap in format chain1 atom1
chain2 atom2 weight(opt) distance(opt)
--scaling_n SCALING_N, -scaling_n SCALING_N
User RNA/DNA defined scaling for mapping to all-atom
contact-map.
--contfunc_n CONTFUNC_N, -contfunc_n CONTFUNC_N
RNA/DNA. 1: LJ C6-C12, 2 LJ C10-C12, 3 LJ C12-C18, 6
Gauss + excl, 7 Multi Gauss . Default: 2
--cutoff_i CUTOFF_I, -cutoff_i CUTOFF_I
User defined Cut-off (in Angstrom) for Protein RNA/DNA
interface contact-map generation. Default: 4.5 Å (for
all-atom) or 8.0 Å (for coarse-grianed)
--cutofftype_i CUTOFFTYPE_I, -cutofftype_i CUTOFFTYPE_I
For Protein RNA/DNA interface. -1 No map, 0 use -cmap
file, 1 all-atom mapped to CG, 2: coarse-grain .
Default: 1
--W_cont_i, -W_cont_i
Weight (and normalize) Protein RNA/DNA interface CG
contacts based on all atom contacts
--cmap_i CMAP_I, -cmap_i CMAP_I
User defined Protein RNA/DNA interface cmap in format
chain1 atom1 chain2 atom2 weight(opt) distance(opt)
--scaling_i SCALING_I, -scaling_i SCALING_I
User Protein RNA/DNA interface defined scaling for
mapping to all-atom contact-map.
--contfunc_i CONTFUNC_I, -contfunc_i CONTFUNC_I
Protein RNA/DNA interface. 1: LJ C6-C12, 2 LJ C10-C12,
3 LJ C12-C18, 6 Gauss + excl, 7 Multi Gauss . Default:
2
--nbfunc NBFUNC, -nbfunc NBFUNC
1: LJ C6-C12, 2 LJ C10-C12, 3 LJ C12-C18 (3: modified
gmx5), (6&7: OpenSMOG)6 Gauss + excl, 7 Multi Gauss .
Default: 2
--excl_rule EXCL_RULE
Use 1: Geometric mean. 2: Arithmatic mean
--nbshift, -nbshift (with --opensmog) Shift the potential (V(r)) by a
constant (V(r_c)) such that it is zero at cutoff
(r_c). Default: False
--interaction, -interaction
User defined interactions in file interactions.dat.
--btparams, -btparams
Use Betancourt-Thirumalai interaction matrix.
--mjparams, -mjparams
Use Miyazawa-Jernighan interaction matrix.
--interface INTERFACE, -interface INTERFACE
User defined multimer interface nonbonded params. Format atype1 atype2 eps sig(A)
--debye, -debye Use Debye-Huckel electrostatic interactions.
--debye_length DEBYE_LENGTH, -debye_length DEBYE_LENGTH
Debye length. in (Å)
--debye_temp DEBYE_TEMP, -debye_temp DEBYE_TEMP
Temperature for Debye length calculation. Default: 298
K
--CA_charge, -CA_charge
Put charges on CA for K,L,H,D,E. Default: False
--CB_charge, -CB_charge
Put charges on CB for K,L,H,D,E. Default: False
--P_charge, -P_charge
Negative charge on Phosphate bead. Default: False
--PPelec, -PPelec Add electrostatic repulsions for Phosphate-Phosphate
beads. Default: False
--iconc ICONC, -iconc ICONC
Solvent ion conc.(N) for Debye length calcluation.
Default: 0.1 M
--irad IRAD, -irad IRAD
Solvent ion rad for Debye length calcluation. Default:
1.4 Å
--dielec DIELEC, -dielec DIELEC
Dielectric constant of Solvent. Default: 78
--dswap, -dswap For domain swapping runs. Symmetrised SBM is
generated.
--sym_intra, --sym_intra
Intra-chain Symmetrised SBM is generated.
--hphobic, -hphobic Generate hydrophobic contacts.
--hpstrength HPSTRENGTH, -hpstrength HPSTRENGTH
Strength with which hydrophobic contacts interact.
Default: 1.0 ε
--hpdist HPDIST, -hpdist HPDIST
Equilibrium distance for hydrophobic contacts.
Default: 5.0 Å
--custom_nuc CUSTOM_NUC, -custom_nuc CUSTOM_NUC
Use custom non native DNA/RNA structure Eg.:
polyT.pdb. Default: Use from native structure
--control Use the native system as control. Use DNA/RNA bound to
native protein site. --custom_nuc will be disabled.
Default: False (Move DNA/RNA away from native binding
site)
- SuBMIT is licensed under the GNU GPL v3 (LICENSE).
- Files in hy36cctbx/ are licensed under an unrestricted open source license by Lawrence Berkeley National Laboratory, University of California (hy36cctbx/LICENSE_2_0.txt). These are not written or modified by SuBMIT team and are derived from the cctbx_project iotbx repository.
- GROMACS 4.5.x: https://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz
- GROMACS 4.6.x: https://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
- GROMACS 4.5.4 SBM1 (Gaussian contact potentials): https://smog-server.org/extension/#gauss
- GROMACS 5.1.4: https://ftp.gromacs.org/pub/gromacs/gromacs-5.1.4.tar.gz
- OpenSMOG v1.1.1: https://github.com/smog-server/OpenSMOG
- OpenSMOGmod (Contact potential for >2 particles): https://github.com/sglabncbs/OpenSMOGmod