Return to Main Documents Page

PDB Rx

Attempts to generate a complete PDB file and PSF topology file from a user supplied PDB file (beta).

Accessibility

The PDB Rx module is accessible from the Build section of the main menu.

Basic Usage

The purpose of this module is to create complete structure and topology files so that the files are ready for simulation using SASSIE and other simulation programs (NAMD, CHARMM) that use the CHARMM force-field.

An input PDB tile used to create a new PDB along with PSF file(s) to so that the system is ready for molecular simulation.

The user supplies a PDB file as input and the contents are analyzed internally using PDB Scan to interpret information provided in the header of the PDB file to determine if a complete structure can be built. The program determines the molecult type for each segment (protein, nucleic acid, or other), maps chains to segments, finds missing atoms/residues for each segment, carries out an analysis of biomt records, and identifies any disulfide bonds.

With this information a complete model is generated and saved as a new PDB file with the appropriate naming convention required for the CHARMM force-field. Additionally, two protein structure files (PSFs) are generated (CHARMM and XPLOR formats). The XPLOR format is required by NAMD.

If the user supplied PDB file has missing or incomplete information in the header (i.e. the non-ATOM records) then the program will analyze the structural information, provide a summary and prompt the user to verify the chain/segment defintions, sequence of each segment, list of disulfide residues, and query for any biomt records. This utility is only partially developed.

Advanced input options allow for users to review the chain to segment definitions, review sequences for each segment and an option to upload FASTA formatted text files to complete sequence information, and to add and/or edit BIOMT records to complete biological units.

Notes

Screen Shots and Description of Input Fields

These examples show the analysis and file output of a run using a PDB input file with header records from the protein data bank.

PDB files without headers are not currently supported.

inline image

Case 1: PDB with Header

This example shows the report for a protein-dna complex, 5E3L.pdb, where the protein is missing atoms and residues.

inline image

The text output region provides a brief summary of the contents of the file. It focusses on issues that might prevent the creation of a correct CHARMM parameterized system (missing residues and atoms and unusual residues not standard in CHARMM). If the PDB is not ready for simulation (as is the case in this example) many of the lines point to the full report for more details.

inline image

The JSmol panes show an interactive rendering of both the input 5E3L.pdb and the final complete structure named 5E3L_charmm.pdb.

In addition, two PSF files are saved in CHARMM and XPLOR format.


Case 2: PDB with Header and Using Advanced Input Options

The Advanced Input variables are listed below.

inline image

After submitted the job the user will be prompted with pop-up windows to determine what advanced options should be used. There are three potential inputs.

PDB Rx Segment Editor

After the intial PDB scan is completed on the user supplied PDB file a report of the segments identified from the chains are presented for review. This identifies key definitions of molecular type (protein, dna, rna, other) and residue ranges. In addition a summary of the compatibility of the user supplied file for CHARMM force-field, the TAMC module, and MD simulation is supplied.

inline image

The user is asked whether they wish to edit these defitions. If the user selects "no" then these defitions are accepted. If the user selects "yes" to edit these defintions the following screen is presented.

inline image

This is a scrollable list of each residue (amino acid or nucleotide) with the defined segment and supplied chain information along with the molecular type (protein, dna, rna, or other).

Note that this may be a very long list if your system is large.

There are four options that can exercised. For the first three, split, join, and rename one should select a single residue (i.e. row) and then click the appropriate button. The fourth option accept can be pressed to save the current state and proceed to the next advanced option, PDB Rx Sequence Editor, discussed below.

PDB Rx Sequence Editor

The next option is to review the sequence of each segment and have an opportunity to upload a FASTA formatted file to indicate a new sequence for each segment. Lower case letters represent residues that are known to be missing from the initial PDB file and upper case residues represent residues with at least partial coordinates in the initial PDB file. The sequences are separated by the segment defintions.

inline image

The user is asked whether they wish to edit these defitions. If the user selects "no" then these defitions are accepted. If the user selects "yes" to edit these defintions the following screen is presented.

inline image

The user is prompted to select a single segment name to then upload a file with the desired sequence for that segment. The file should be formated using the standard FASTA format.

After upload one or more files, the user presses done to continue. Note that one can press done prior to uploading files which would accept the original sequences reported.

PDB Rx Biomt Editor

The next option is to review the biomt records and potentially add and/or edit biomt records.

inline image

The user is asked whether they wish to edit these defitions. If the user selects "no" then these defitions are accepted. If the user selects "yes" to edit these defintions the following screen is presented.

inline image

The user can select one or more segments to assign a new biomt record. One can also click skip to exit the option without altering the original biomt record(s).

Note that on different operating systems and browsers to select non-adjacent rows one has to use different keystrokes. Using Safari on a Macintosh one can use "command-click" while using Chrome on Windows one can use "control-click".

Once submit is pressed then the following input screen is provided to define the matrix elements of the rotation and translation sections of the newly defined biomt record.

inline image

After editing this record press submit to accept the values.

The JSmol panes show an interactive rendering of both the input 5E3L.pdb and the final complete structure named 5E3L_charmm.pdb.

In addition, two PSF files are saved in CHARMM and XPLOR format.


Reference(s) and Citations

Return to Build

Return to Main Documents Page

Go to top