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.
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.
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.
MET 1 ILE 2 GLU 3 ASP 4 PRO 5 ......
| 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
|
| 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. |
| 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
|
| 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). |
| 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). |