PSF (CHARMM, NAMD, or XPLOR protein structure file)¶
Topology parser |
A protein structure file (PSF) contains topology information for CHARMM, NAMD, and XPLOR. The MDAnalysis PSFParser only reads information about atoms, bonds, angles, dihedrals, and impropers. While PSF files can include information on hydrogen-bond donor and acceptor groups, MDAnalysis does not read these in.
Important
Atom ids
Although PSF files index atoms from 1 in the file, the MDAnalysis PSFParser subtracts 1 to create atom ids. This means that if your atom is numbered 3 in your PSF file, it will have an Atom.id of 2 in MDAnalysis.
Atom indices are MDAnalysis derived and always index from 0, no matter the file type.
Reading in¶
PSF files can come in a number of “flavours”: STANDARD, EXTENDED, and NAMD. If your file is not a standard file, it must have a NAMD or EXT flag to tell MDAnalysis to how to parse the atom section.
As a NAMD file is space-separated, files with missing columns can cause MDAnalysis to read information incorrectly. This can cause issues for PSF files written from VMD.
PSF files can encode insertion codes. However, MDAnalysis does not currently support reading PSF files with insertion codes.
PSF specification¶
CHARMM
Normal (standard) and extended (EXT) PSF format are supported. CHEQ is supported in the sense that CHEQ data is simply ignored.
CHARMM Format from source/psffres.src:
CHEQ:
II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I),ECH(I),EHA(I)
standard format:
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8,2G14.6)
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR
expanded format EXT:
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR
no CHEQ:
II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I)
standard format:
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8)
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8) XPLOR
expanded format EXT:
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8)
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR
NAMD
This format is space separated (see the release notes for VMD 1.9.1, psfplugin).