psf2top Usage

Example run

For a protein+lipid psf system, the GROMACS topology can be generated by the follwing command. This assumes that the name of the psf file is system.psf and you have the necessary parameter files in the same directory.

$ psf2top.py -p system.psf -c par_all36_prot.prm par_all36_lipid.prm

You can add -v for debug information.

Notes

• psf2top.py converts the psf file to GROMACS topology format. It creates one top.top plus one or more itp files. Each segment in the psf file is converted to one itp file.

• If you have disulfide bridges in the system:
  ** After patching the S-S bonds during psf preparation (using psfgen or autopsf), make sure to regenerate angles and dihedrals after patches.
  ** Also make sure that the residues that share a S-S bond are both in the same segment in the psf file.

• Input formats that psf2top.py can read (see also here):

  ** PSF files:    
     ** If generated using VMD/psfgen, are OK and readable.
     ** If created using X-PLOR or CHARMM, they are not readable. First convert them to the above form using psfgen.
    
  ** PAR files:
     ** CHARMM-format is OK and readable.
     ** X-PLOR format is not currently supported.

  ** STR file (CHARMM stream files): readable as parameter files.

• You should provide all of CHARMM parameter files for the atoms in your psf file. These correspond to the parameter files that you use for your system when running the NAMD simulation.

• For the CHARMM parameter files, theHBOND sections is ignored.

• If you use CHARMM-GUI to generate inputs, make sure to use the generated .xplor format for the psf file.

• Remove water molecules from the psf file before conversion. Fully converting water molecules to the gromacs format requires adding SETTLE for water which is not implemented yet.

• You can use editconf and genbox to add water to the system later on in GROMACS:

  • Make sure to add the appropriate itp files for the water and ions to the top.top file.
  • You need to add #define _FF_CHARMM to the beginning of the topology file if you're using charmm27.ff water models.
  • Also add the necessary atom types (for the chosen water model and ions) at the end of [atomtypes] in the top.top file.