
Generating PSF file and initial coordinates

1) use seq2psf to generate psf files from 3-character sequences:

  a) generate a protein psf file

        % seq2psf PROT1.seq

          ->  creates PROT1.psf

  b) generate a psf file for 20-bp DNA. 

        % seq2psf DNAone.seq

          ->  creates DNAone.psf

  c) rna: need command-line options:

        % seq2psf -rna RNA1.seq 

          ->  creates RNA1.psf

    to get all command-line options:
        % seq2psf --help-script

2) use pdb2psf to generate psf file from a pdb file:

     % pdb2psf 1bph.pdb

       -> creates 1bph.psf

    to get all command-line options:
         pdb2psf --help-script

3) generating initial (extended chain) coordinates

   % xplor -py genExtendedDNA.py

       -> creates dna1_extended.pdb

      take a peak at this using:
          % vmd-xplor -noxplor dna1_extended.pdb

      to quit:
              Control --> Quit -> xplor and vmd

4) adding atoms to existing structure (e.g. from the PDB database).
   In this case, generate atoms for a modified amino acid.

   % xplor -py addAtoms.py

       -> creates new.psf and new.pdb

      take a peak at this using:

          % vmd-xplor -noxplor start.pdb new.pdb

     display only the mutated residue
        *Molecule --> Drawn --> set selection
           type: resid 182


      to see which atoms have been added click yellow indicator next to
      the red new.pdb button in the molecule window. The view may need to be
      rotated.



5) adding disulfide bonds to pre-existing structure (1rop.pdb)

   % xplor -py testDiS.py

       -> creates testDiS.psf
         
      compare testDiS.psf with the output of

        % pdb2psf 1rop.pdb

      i.e.:
        % grep -e NATOM -e NBOND testDiS.psf 1rop.psf

6) generate very basic psf and parameter files for a HETATM residue. 
   Currently, CONECT records are not read, so the whole residue (ligand)
   must be grouped as a rigid body.

  This example generates psf+parameters for a heme group (including iron)

  % ./genLigand.py  -segid B -resid 147 1gbv.pdb

      -> creates HEM.top, HEM.par and HEM.psf


