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)
https://colab.research.google.com/github/digvijaylp/submit/blob/main/SuBMIT.ipynb
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 (Reddy and Thirumalai, 2017. https://doi.org/10.1021/acs.jpcb.6b13100)
$ python submit.py --reddy2017 --aa_pdb [All-atom .pdb file]
$ python submit.py --reddy2017 --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
--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
--reddy2017, -reddy2017, --sopsc2017, -sopsc2017
Reddy & Thirumalai 2017 SOP-SC CA-CB.
10.1021/acs.jpcb.6b13100
--denesyuk2013, -denesyuk2013, --rna_tis2013, -rna_tis2013
Denesyuk & Thirumalai 2013 Three Interaction Site TIS
P-S-B model. 10.1021/jp401087x
--chakraborty2018, -chakraborty2018, --dna_tis2018, -dna_tis2018
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
Banerjee & Gosavi 2023 Self-Peptide model.
10.1021/acs.jpcb.2c05917
--virusassembly, -virusassembly, --capsid, -capsid
Preset for structure based virus assembly (inter-
Symmetrized)
--dlprakash, -dlprakash, --duplexpair, -duplexpair
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 code 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