123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306  READ keywords END One of these sections must be present for every molecule involved in the APBS calculation. Molecule and "map" IDs are assigned implicitly assigned for each molecule/map read, based on order and starting at 1. This section has the following keywords: mol format path This command specifies the molecular data to be read into APBS. The arguments are: format The format of the input data. Acceptable flags include: pqr Molecular data is in PQR format pdb Molecular data is in PDB format. We do not completely follow the PDB format, as specified in the above link. Specifically, we allow general whitespace-, tab-, or newline-delimited format, thereby permitting the manipulation of molecules with coordinates outside the ±999 range. Beginning with APBS 0.5.0, the optional use of the chain ID field is now supported in both PDB and PQR formats. path The location of the molecular data file. This pathname should not include spaces. parm format path This command specifies the charge and radius data to be used with PDB-format molecule files. The arguments are: format The format of the parameter file. Acceptable flags include: flat APBS flat-file parameter format xml APBS XML parameter format path The location of the parameter data file. This pathname should not include spaces. diel format path-x path-y path-z This command allows APBS to read the dielectric function \epsilon(x) mapped to 3 meshes shifted by one-half grid spacing in the x, y, and z directions. The inputs are maps of dielectric variables between the solvent and biomolecular dieletric constants; these values are unitless. In general, this command will read dielectric maps written by write commands in earlier APBS calculations. NOTE: if you choose this option and have a non-zero ionic strength, you must also include a read kappa statement Arguments for this command are: format The format of the dielectric map. Acceptable values include: dx OpenDX format (see Formats section) path-x The location of the x-shifted dielectric map file. This pathname should not include spaces. path-y The location of the y-shifted dielectric map file. This pathname should not include spaces. path-z The location of the z-shifted dielectric map file. This pathname should not include spaces. kappa format path This command allows APBS to read the ion-accessibility function \overline{\kappa}^2(x) mapped to a mesh. The inputs are maps of ion accessibility values which range between 0 and the build Debye-Hückel screening parameter; these values have units of Å-2. In general, this command will read kappa-maps written by write commands in earlier APBS calculations. NOTE: if you choose this option, you must also include a read diel statement Arguments for this command are: format The format of the kappa map. Acceptable values include: dx OpenDX format (see Formats section) path The location of the kappa map file. This pathname should not include spaces. charge format path This command allows APBS to read the fixed (molecular) charge density function mapped to a mesh. The inputs are maps of charge densities; these values have units of ec (electron charge) per Angstrom3. In general, this command will read charge-maps written by write commands in earlier APBS calculations. Arguments for this command are: format The format of the charge map. Acceptable values include: dx OpenDX format (see Formats section) path The location of the charge map file. This pathname should not include spaces. mesh format path This command allows APBS to read a finite element mesh to use as a starting point for finite element calculations. The input is simply the mesh geometry; e.g., as produced by a finite element mesh generation program such as LBIE-Mesher or GAMer. Arguments for this command are: format The format of the input mesh. Acceptable values include: mcsf MCSF format (description coming soon!) path The location of the meshes file. This path should not include spaces.