About Coarse-Grained Model

Force Field Description for Cα

A Gō-like CG model1–4 used for reducing the resolution of protein models for simulation while maintaining key energetic properties. Each amino acid is replaced by a CG bead at is \(C_\alpha\) site. The potential energy function is modified to use a Lennard Jones 12-10-6 Van der Waals potential5 that accounts for the devsolvation barrier between two amino acids and a double-well angle potential6 which is designed to capture the transition between α-helices and β-sheets. The function is as follows: \[E_{tot} = E_{bond} + E_{angle} + E_{dihedral} + E_{elec} + E_{vdW}\] \[E_{tot} = \sum_i K_b(b_i−b_0)^2 + \sum_i −\frac1\gamma ln \{e^{−\gamma[K_\alpha(\theta_i−𝜃_\alpha)^2+\epsilon_\alpha]} + e^{−\gamma K_\beta (\theta_i−\theta_\beta)^2}\}+\sum_i \sum_{j=1}^4 K_{D_j}[1 + cos(j\Psi_i− \delta_j)] + \sum_{i,j}𝜀_{ij}[13(\frac{R_{ij}}{r_{ij}})^{12} − 18(\frac{R_{ij}}{r_{ij}})^{10} + 4(\frac{R_{ij}}{r_{ij}})^6]\] where \(K_b\) is the bond force constant and equals 50 \(kcal/mol/Å^2\); \(b_i\) is the \(i^{th}\) pseudo bond length between two adjacent beads; \(b_0\) is the equilibrium pseudo bond length and set as 3.81 Å, which is the average distance between two adjacent \(C_\alpha\) atoms in the protein sequence; 𝛾, \(K_\alpha\), \(\theta_\alpha\), \(\epsilon_\alpha\), \(K_\beta\) and \(\theta_\beta\) are all constants of the double-well angle potential6, which is designed to capture conformational transitions between α-helix and β-sheet; \(\theta_i\) is the \(i^{th}\) angle of two adjacent pseudo bonds; \(K_{D_j}\) and \(\delta_j\) are the dihedral force constant and the phase at periodicity j, respectively; \(\Psi_i\) is the \(i^{th}\) pseudo dihedral angle; \(q_i\) is the net charge of the \(i^{th}\) bead, which equals the net charge of the corresponding amino acid residue; \(\epsilon_\theta\) and \(\epsilon_\gamma\) is the dielectric constants of vacuum and water, respectively; \(l_D\) is the Debye length and set as 10 Å4; \(\epsilon_{ij}\) and \(R_{ij}\) are the well depth and the vdW radius respectively in the LJ 12-10-6 potential5, which takes into account of desolvation barriers, of the interaction between beads \(i\) and \(j\) and \(r_{ij}\) is their distance. The nonbonding interactions are smoothly switched to zero starting at the distance of 18 Å and ending at 20 Å. Parameters \(\epsilon_{ij}\) and \(R_{ij}\) are set according to the interaction types. For the beads that have native contacts, \(\epsilon_{ij} = \epsilon_{ij}^{HB} + \eta_{scale}\cdot\epsilon_{ij}^{SC−SC} + \epsilon_{ij}^{BB−SC}\), where the hydrogen bond (HB) contact well depth \(\epsilon^{HB}_{ij}\) is set as 0.75 kcal/mol for a single HB contact and 1.5 kcal/mol for multiple HB contacts7; the sidechain-sidechain (SC-SC) interaction well depth \(\epsilon^{SC-SC}_{ij}\) is set as the Bentancourt−Thirumalai statistical potential8 and then scaled by a multiplicative factor \(n_{scal}\) to achieve a realistic native-state stability for the particular protein; the backbone-sidechain (BB-SC) interaction well depth \(\epsilon^{BB-SC}_{ij}\) is set as 0.37 kcal/mol7. All the native contacts are identified for the residue pairs that are separated by no less than 2 residues within the native structure. The native HB contacts are identified by STRIDE9. The native SC-SC contacts and BB-SC contacts are identified by collecting those contacts where the minimum contact distance is less than 4.5 Å. The value of \(R_{ij}\) for a native contact is set as the native distance \(d_{ij}\) between beads \(i\) and \(j\). For the non-native contacts, to make the interaction mostly repulsive , we use \(\epsilon_{ij} = \sqrt{\epsilon_i\cdot\epsilon_j}\) and \(R_{ij} = R_i + R_j\), where \(\epsilon_i\) is set as 0.000132 kcal/mol7 and \(R_i\) is set as the non-native collision diameter \(\sigma_i\) of beads \(i\) multiplied by \(2^{1/6}\) and divided by 2. The collision diameters are calculated based on the protein’s native structure according to Karanicolas−Brooks model5.

Force Field Description for Cα-SCM

This model uses two interaction sites per residue, one centered on the alpha carbon and the center of mass of the side chain. Non-bonded potentials are applied to those interaction sites separated by 4 or more covalent bonds7. The potential energy is calculated as above, with both backbone and sidechain contacts.

How to Use the Web Application

PDB files

User can upload PDB files or provide PDB IDs. If a PDB ID is provided, the PDB file will be downloaded from rcsb.org.

The current version only supports PDB files that contain a single chain or model. And the Cα-SCM model only accepts one PDB file.

If a PDB file is missing atoms, choose to "Rebuild PDB" on the submission page and upload a seq file that contains amino acid sequences. A sample seq file is shown below.


Parameters applied to all monomers

Parameter Description Value
N scale Scaling factor for the energy between native contacts. Positive number, usually between 1 and 2.
Model type Number of interaction sites per residue (1 site = Cα, 2 sites = Cα-SCM). Select from
  • ca: Cα model;
  • casm: Cα-SCM model.
fnn Scaling factor for sidechain radii.
NBXMOD Minimum number of bonds between sites before they are in the nonbonded list. See https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/nbonds/. Select from 0, 1, 2, 3, 4, 5.
Note that 3 and 4 are the most frequently used values.
Cutoff for sidechain heavy atom contact Maximum separation between two atoms to still be counted as a native contact. Default 4.5 Å. Must be positive.

Parameters specific to each monomer

Parameter Description Value
Segment ID Single letter identifier for that chain. If using multiple chains, this needs to be unique. A-Z.
Potential type Type of potential to use to calculate interactions between amino acids. See bt, mj, kgs. Select from
  • bt;
  • mj;
  • kgs.
Use go model bond length Whether to use transferable go bond length of 3.81 Å. Otherwise, use non-transferable bond lengths from PDB. Yes/No (default No).
Use a go model dihedral potential Whether to use transferable go model dihedral potentials. Yes/No (default No).
Include electrostatics Whether to include electrostatic interactions. Yes/No (default Yes).
Use double-well angle potential Whether to use the double-well angle potential (ETEN) described above (Yes), or to revert to the default 6-12 potential (No). See https://www.charmm.org/charmm/documentation/by-version/c40b1/params/doc/energy/, specifically the section titled “The 10-12 van der Waals potential”. Yes/No (Default Yes).

Output files

File Description
[pdb-file-name]_ca.cor Standard CHARMM coordinate file that contains the XYZ coordinates of all the atoms.
[pdb-file-name]_ca.psf Standard CHARMM protein structure file that indicates what atoms are involved in bonds, angles, dihedrals, and improper dihedrals.
[pdb-file-name]_ca.top Standard CHARMM residue topology file that indicates what atom types compose each residue.
[pdb-file-name]_[nscal]_[fnn]_go_[pot].prm Standard CHARMM parameter file that contains all the constants and parameters from the force fields above.
[pdb-file-name]_ca.seq Contains the protein sequence with 3 letter codes and space separation.
[pdb-file-name]_ca_mini.cor Standard CHARMM coordinate file that has undergone 10,000 steps of minimization to relax the structure.
[pdb-file-name]_[nscal]_[fnn]_go_[pot].xml Contains same information as the parameter file in the xml format.
job.log Contains a record of inputs, as well as all information printed to screen, including error messages (if applicable).


  1. Nissley, D. A.; O’Brien, E. P. Structural Origins of FRET-Observed Nascent Chain Compaction on the Ribosome. J. Phys. Chem. B 2018. https://doi.org/10.1021/acs.jpcb.8b07726.
  2. Fritch, B.; Kosolapov, A.; Hudson, P.; Nissley, D. A.; Woodcock, H. L.; Deutsch, C.; O’Brien, E. P. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis. J. Am. Chem. Soc. 2018. https://doi.org/10.1021/jacs.7b11044.
  3. Leininger, S. E.; Trovato, F.; Nissley, D. A.; O’Brien, E. P. Domain Topology, Stability, and Translation Speed Determine Mechanical Force Generation on the Ribosome. Proc. Natl. Acad. Sci. U. S. A. 2019. https://doi.org/10.1073/pnas.1813003116.
  4. O’Brien, E. P.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M.; O’Brien, E. P.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M.; O’Brien, E. P.; Christodoulou, J.; et al. Trigger Factor Slows Co-Translational Folding through Kinetic Trapping While Sterically Protecting the Nascent Chain from Aberrant Cytosolic Interactions. J. Am. Chem. Soc. 2012, 134 (26), 10920–10932. https://doi.org/10.1021/ja302305u.
  5. Karanicolas, J.; Brooks, C. L. The Origins of Asymmetry in the Folding Transition States of Protein L and Protein G. Protein Sci. 2002. https://doi.org/10.1110/ps.0205402.
  6. Best, R. B.; Chen, Y. G.; Hummer, G. Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor. Structure 2005. https://doi.org/10.1016/j.str.2005.08.009.
  7. 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. 2008. https://doi.org/10.4404/hystrix-28.2-12255.
  8. Betancourt, M. R.; Thirumalai, D. Pair Potentials for Protein Folding: Choice of Reference States and Sensitivity of Predicted Native States to Variations in the Interaction Schemes. Protein Sci. 1999, 8 (2), 361–369. https://doi.org/10.1110/ps.8.2.361.
  9. Frishman, D.; Argos, P. Knowledge‐based Protein Secondary Structure Assignment. Proteins Struct. Funct. Bioinforma. 1995, 23 (4), 566–579. https://doi.org/10.1002/prot.340230412.