/ MIBPB from Wei Group

MIBPB is a software package for obtaining electrostatic potential and solvation free energy via solving the Poisson-Boltzmann (PB) equation. It makes use of the second order convergent MIB technique and is essentially grid independent. Its mean relative error is less than 0.5% for about 1000 test proteins when the grid size is refined from 1.1 to 0.2 Armstrong.      [User Manual]

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Outerior Dielectric
Grid Resolution
Ion Strength
Surface Probe Radius for MIBPB
Linearized PB:
Simplified Solver:
Probe Radius
Grid Resolution
Grid Extension
Force Field:
Protonation: at pH: by:
Remove Water:  Yes
Remove Hydrogen:  Yes
Only assign charges and radius:  Yes
Charge Type:
Radius Type:
Residue Type:
Residue ID:     
     
Show molecule as: Color as:
JMol Surface: Translucent: Color:
ESP min: max: Scale



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User Guide
  Take your results:
  • Using Email: The link for your result will be sent to your email address when you submit your job with your email information. We strongly recommend the users to use the email to receive the result link! You can open the link and use the "Download Result" button under the molecular visualization window to obtain more results. The results are saved in a compacted zip file, including a log file containing the result of MIBPB, a dx file containing the electrostatic information, and your input file. The surface results, PDB2PQR result and PROPKA result are also included when you use the corresponding process.
  • Without Email: After you submit your job, your browser will be redirected to a web page and refresh until the job is done. You can wait at that web page or save its link for reopening it later. When the job is done, the web page will be redirect to the result web page automatically. You can download your result the same as the "Using Email" method mentioned above.

  Input Options and Submit Job Options:
  • PDB ID: You can use our server to automatically download the PDB file via giving its 4-digit ID, such as 1AJJ. You can also give the chain ID to perform calculation only on this chain. The chain ID can be A, B, C, D and so on. We also support the syntax "A-D" to assign sequential chain IDs. If user gives chain ID as *, -, All or even blank, the server will use all the chains in the PDB file.
  • User File: User can upload a prepared PQR file to perform calculation. PDB file for a biomolecule and a PDB/Mol2 file for a small molecule are also supported after our automatic preparation.
  • Submit button: Submit the job to server for MIBPB calculation.
  • Default: Reset all the parameters.
  • Clear Job: If you want to submit a new job, this function allows you to reset everything.

  MIBPB Options:
  • Interior Dielectric: The dielectric constant in solute, the default value is 1.0 in the MIBPB package.
  • Outerior Dielectric: The dielectric constant in solvent, the default value is 80.0 in the MIBPB package.
  • Grid Resolution: The grid size utilized in the discratization of the PB equation. In the current PB solver it is restricted in the interval [0.2, 1.2], the default value is 0.8.
  • Ion Strength: The ionic strength of the solvent, in the unit mol/L. The default value is 0.
  • Probe Radius: The probe radius used for surface generation, the range of this value is [0.8, 2.0] in the current version of the MIBPB package. Default 1.4.
  • Linearized PB: Indicator of using linearized PB or non-linearized PB. Note that the non-linearized PB only for the case that kappa1 > 0. Default is Linerized PB.
  • Simplified Solver: Indicator of using the MIBPB solver or the simplified solver. Default is MIBPB solver(unchosen).

  Resulting Surface Options:

      The resulting surface option can help to additionally generate a surface for viewing the electrostatic results. The surface result will be added into your compressed zip result file. You can view the surface and electrostatic result in other visualization software. If you do not need the surface result, you can deselect the checkbox after "Resulting Surface Options".
      User can use our new ESES algorithm to generate the solvent-excluded surface. Even the surface file is not reported during the computation, the user can also use our visualization tool (JSMol) to generate a surface.

  • Probe Radius: The probe radius used for surface generation in the surface result. The range of this value is not less than 0.5 here, default 1.4.
  • Grid Resolution: The grid size for generating the surface result. The default value is 0.8. You do not need to set this value as that in MIBPB calculation because the surface is generated independently.
  • Grid Extension: It's the option for the buffer size outside the input molecule when using ESES surface. The default value is 2.0.

  PDB2PQR Options:

     The PDB2PQR program is introduced to deal with the PDB input files. When you submit a PDB file, PDB2PQR could help you convert the PDB file to PQR file with charges and atomic radius information. The hydrogen atoms could be added during this process. The PROPKA 3.0 is also used to protonate the atoms at a certain pH value within PDB2PQR program. Thanks to the support from Dr. Nathan Baker and his group! More information about PDB2PQR can be obtained from PDB2PQR webserver.

  • Force Field: The force field to be used for process the PDB file. Six force fileds can be used in PDB2PQR: AMBER, CHARMM, PARSE, PEOEPB, SWANSON and TYL06.
  • Protonation: The method for protonation at given pH. The default method for protonation is the PROPKA 3.0. If your structure has been protonated before, you can choose "Don't use" in the method.
  • Remove Water: Remove waters before processing protein. Default is to remove water in our server (different to PDB2PQR server). Currently recognized and deleted are the following water types: HOH, WAT.
  • Remove Hydrogen: Remove exist explicit hydrogen atoms in the structure. Default is not to remove hydrogen. The explicit hydrogen will be kept in PDB2PQR in default. If you choose this option, the hydrogen atoms will be removed before PDB2PQR process and new hydrogen atoms will be added in the PDB2PQR.
  • Only assign charges radii: Only assign charges and radii, and do not add atoms, debump, or optimize. It's suitable when your structure has been prepared before and you just want to add charges and radii based on the force field. It may help to fix some failure in PDB2PQR.
  • Notice: If you choose certain chains to be processed or to remove hydrogen, the origin PDB file will be modified in our server and only the atoms with alternate location indicator "A" will be saved to avoid uncertain atom postion. If you encounter any problem, please send an email to webmaster for help.

  Small Molecule to PQR Options:

     The AmberTool14 is introduced to deal with the small molecule input files. When you submit a PDB file or mol2 file containing small molecule, Antechamber program could help you to calculate the atom charges of the molecule and further help to use the GAFF force filed to assign the parameters. More information about Antechamber can be obtained from Antechamber. Our server will generate the pqr file for small molecule and also the Amber input frcmod, prmtop and inpcrd files for the users.

  • Charge Type: We support three types of atom charges in Amber14, including AM1-BCC(default),Gasteiger and Mulliken.
  • Radius Type: We support five sets of atom radius in Amber14, including mbondi(default),mbondi2, mbondi3, bondi, amber6.

  pKa Options:

      The pKa of a chosen residue can be calculated in our server. Limited by the function of PDB2PQR, the arginine (ARG) can't work until now. The Interior Dielectric and Outerior Dielectric are important for pKa calculation. In default, when the pKa calculation is chosen, the interior dielectric is set to 20 and outerior dielectric is set to 80. The result depends on the interior dielectric constant relative to the protein electrostatic. Now the pKa calculation only support the user uploaded PDB/PQR file or online PDB file. After pKa calculation, the calculated pKa will show below the molecular viewer window. The surface generation function will be disabled in pKa calculation.

  • Residue Type: The type of residue to be calculated. You can choose the Residue ID only after you select a residue type.
  • Residue ID: The exact residue ID for calculatiton. If input file is downloaded from PDB online, the user can use Analyze online PDB to analyze the exact residue information. In case of uploading a user file, the residue ID will be shown after you select a certain input file. It contains the "chain:resname resid" information.

  Other Options:
  • Job Title: The job title for the MIBPB calculation. It is used to distinguish your results when you need to run many jobs.
  • User Email: TThe link of the result will be sent to the user email. You can open the link in the email to view and download your result. We recommend you to use the email function when the job may take a long time.

  View Results Online:
  • Molecular Visualization: You can change the mode and color for the visualization of your molecule. The molecule can be shown as: Cartoon, Rocket, Ribbon, MeshRibbon, Trace, Backbone, Ball&Stick, Wireframe and Space Fill by selecting the "Show molecule as" option under the visualization window. The color for the molecule can also be chosen by the "Color As" option.
  • Surface Options: You can visualize the surface based on the JMol method or the surface calculated by ESES during the computation. The JMol surface can be generated or deleted by the "JMol Surface" option. You can generate vdW surface (very fast), solvent accessible surface, solvent excluded surface and molecular surface by JMol. You can also control the surface showing as dots or mesh in this option after you generate a surface. The calculated surface in your job can be loaded by "Load Surface" button. The loaded surface depends on the options in "Surface Options" panel. The transparency and color for surface can also be controlled by the "Translucent" and "Color" panel, respectively. The larger value the translucent is, the more transparent the surface is.
  • Electrostatic Potential (ESP) Visualization: The electrostatic potential result will be saved in the *.dx format. The ESP result can be mapped onto current surface by clicking the "Load ESP"button. You can also load all your results including the calculated surface and ESP by clicking the "Load All"button. The color scheme for the surface based on ESP mapping can be controlled by the "Color" option in the surface option. The BWR, RWB, RGB, High, Low and Rainbow scheme can be used for ESP coloring. The range of the ESP values for coloring can be easily control by the ESP min/max options by either entering the exact value or using the scroll bar.
  • Download Results: You can download all your result files in compacted zip file by clicking the "Download Result" button. You can also download the Jmol format file or PNG format file to re-visualize your result in JMol. A ".jmol" file is simply a ZIP file that can be dragged back into this applet or the Jmol app to recreate the exact state when it was created.

  Server Update:
  • Known Problems: ARN(ARG-H) don't support in PDB2PQR; Molecule too large will fail because of low performance of server


  Reference:
  1. Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng and Guo-Wei Wei. MIBPB: A software package for electrostatic analysis. J. Comput. Chem. 2011, 32, 756–770.
  2. Y.C. Zhou, M. Feig and G.W. Wei. Highly accurate biomolecular electrostatics in continuum dielectric environments. J. Comput. Chem. 2008, 29, 87-97.
  3. W.H. Geng, S.N. Yu and G.W. Wei. Treatment of charge singularities in implicit solvent models. J. Chem. Phys. 2007, 127, 114106 (20 pages).
  4. S. N. Yu, W. H. Geng and G.W. Wei. Treatment of geometric singularities in implicit solvent models. J. Chem. Phys., 2007, 126, 244108 (13 pages).

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