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1 Building Systems

1.1 Preparing PDB files with pdb4amber

Amber Information Flow
Figure 1.1: Basic information flow of Amber

Learning Outcomes

  • Understand the opening steps in the basic information flow in Amber
  • Understand the basic syntax of the pdb4amber command

  • Introduction

    This is not really a tutorial, but instead a page meant to highlight the existence of pdb4amber. It used to be a little difficult to load pdb files into LEaP, especially RNA molecules, which sometimes use disparate naming conventions in the pdb files. Proteins also have missing sections, disulfide bonds and different HIS protonation states, to name a few of the issues. pdb4amber highlights these issues, which require more careful attention, as is pointed out in Tutorial 1.4 Building Protein Systems in Explicit Solvent. pdb4amber analyses and cleans PDB files for further usage, especially within the LEaP programs of Amber. To learn more about the pdb4amber command, please look through section 12.4 on page 205 of the Amber 2020 Manual.

    To get a sense for the capabilities of pdb4amber, type

    %pdb4amber -h 
    usage: pdb4amber [-h] [-i FILE] [-o FILE] [-y] [-d] [-s STRIP_ATOM_MASK]
                     [-m MUTATION_STRING] [-p] [-a] [--constantph]
                     [--most-populous] [--keep-altlocs] [--reduce]
                     [--no-reduce-db] [--pdbid] [--add-missing-atoms]
                     [--model MODEL] [-l FILE] [-v] [--leap-template]
                     [--no-conect] [--noter]
    positional arguments:
      input                 PDB input file (default: stdin)
    optional arguments:
      -h, --help            show this help message and exit
      -i FILE, --in FILE    PDB input file (default: stdin)
      -o FILE, --out FILE   PDB output file (default: stdout)
      -y, --nohyd           remove all hydrogen atoms (default: no)
      -d, --dry             remove all water molecules (default: no)
                            Strip given atom mask, (default: no)
                            Mutate residue
      -p, --prot            keep only protein residues (default: no)
      -a, --amber-compatible-residues
                            keep only Amber-compatible residues (default: no)
      --constantph          rename GLU,ASP,HIS for constant pH simulation
      --most-populous       keep most populous alt. conf. (default is to keep 'A')
      --keep-altlocs        Keep alternative conformations
      --reduce              Run Reduce first to add hydrogens. (default: no)
      --no-reduce-db        If reduce is on, skip using it for hetatoms. (default:
                            usual reduce behavior for hetatoms)
      --pdbid               fetch structure with given pdbid, should combined with
                            -i option. Subjected to change
      --add-missing-atoms   Use tleap to add missing atoms. (EXPERIMENTAL OPTION)
      --model MODEL         Model to use from a multi-model pdb file (integer).
                            (default: use 1st model). Use a negative number to
                            keep all models
      -l FILE, --logfile FILE
                            log filename
      -v, --version         version
      --leap-template       write a leap template for easy adaption (EXPERIMENTAL)
      --no-conect           Not write S-S conect record
      --noter               Not writing TER


    1. Download a PDB file

    We will use the RCSB Protein Databank to download 1ESH, the NMR structure of a small RNA triloop from Brome Mosaic Virus. Go to the pdb databank and type the PDBID into the search bar.

    PDB Databank

    Click on the actual entry. You will see a blue Download Files icon. Click on it and select the pdb file.

    PDB Databank

    The pdb file contains only the lowest energy structure of 1ESH. It still has its header information on it.

    2. Convert the PDB file to Amber format using pdb4amber

    > pdb4amber 1esh.pdb > 1esh.amber.pdb

    Summary of pdb4amber for: 1esh.pdb

    The following (original) chains have been found:

    ---------- Alternate Locations (Original Residues!))

    The following residues had alternate locations:

    ---------- Mising heavy atom(s)


    Click on the filename to download the processed file 1esh.amber.pdb.


    Having completed the first 2 steps of Figure 1.1, you are ready to make topology (prmtop) and coordinate (inpcrd) files using LEaP. For more information on topology and coordinate files as well as the flow of information in Amber, please read through section 1.1 on page 13 of the Amber 2020 Manual.

    To do so, you will have to load a force field which describes the potential energy of the molecules in your system. Different force fields are used for different types of molecules (e.g., DNA, RNA, proteins, lipids, carbohydrates). To learn more about force fields, please refer to section 3 on pages 35 through 62 of the Amber 2020 Manual.

    For more information about building systems with LEaP, go back to the Building Systems tutorial page and find information relevant for your system.

    By Jan Ziembicki and Maria Nagan

    "How's that for maxed out?"

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