parm
Load a topology file.
parm [{[TAG] | name }]
[{ nobondsearch | [bondsearch ] [searchtype {grid|pairlist}] }]
[nomolsearch]
[renumresidues]
<filename> Parameter file to read in; format is auto-detected.
[TAG] Optional tag (bounded in brackets) which can be referred to in place of the topology file name in order to simplify references to it (see examples of how to use tags).
[name ] Optional name that can be used to refer to the topology in place of the file name.
[bondsearch ] Optional; when searching for bonds via geometry search (default for Topologies without bond information) add to distances (default 0.2 Å). Increase this if your system includes unusually long bonds.
[searchtype {grid|pairlist}] Change search algorithm from the default search between residues algorithm:
grid Uses a grid when searching for bonds between residues. This can find bonds between residues that are not sequential (e.g. disulfide bonds).
pairlist Uses a pair list to search for bonds between atoms. This can potentially find bonds across periodic boundaries, but is the more experimental of the two.
Advanced Options – Not recommended for general use
[nobondsearch] If specified do not search for bonds via geometry if Topology does not include bond information. May cause some Actions to fail.
[nomolsearch] If specified do not search for molecule information. May cause some Actions to fail.
[renumresidues] If specified, ensure that any residue cannot be part of more than 1 molecule (can occur with e.g. alternate sites). Residues will be renumbered according to molecule information in that case.
Read in parameter file. The file format will be auto-detected. Current formats recognized by CPPTRAJ are listed here. If the file does not contain bond information, CPPTRAJ will attempt to assign bonds based on a simple distance search of atoms within and between residues. The distance cutoff for determining bonds between atoms
depends on the elements of the two atoms in question, augmented by <offset>. Molecule information is then determined from bond information.
PDB format:
[pqr] [readbox] [conect] [noconect] [link] [nolink] [keepaltloc ]
[pqr] Read charge and radius information from the occupancy and B-factor columns.
[readbox] Read unit cell information from CRYST1 record if present.
[conect] Read CONECT records if present (default).
[noconect] Do not read in CONECT records from PDB file.
[link] Read LINK records if present.
[nolink] Do not read LINK records if present (default).
[keepaltloc ] If specified, only keep alternate atom location IDs matching the specified character .
IMPORTANT NOTES FOR PDB FILES
In some older format PDB files (before version 3), certain atoms may contain the asterisk (’*’) character in their name (e.g. ’C1*’ in a nucleic acid backbone). Since in cpptraj the asterisk is a reserved character for atom masks all asterisks in PDB atom names are replaced with single quote (’) to avoid issues with the mask parser. So in a structure with an atom named C1*, to select it use the mask “@C1”’.
Sometimes PDB files can contain alternate coordinates for the same atom in a residue, e.g.:
ATOM 806 CA ACYS A 105 6.460 -34.012 -21.801 0.49 32.23 ATOM 807 CB ACYS A 105 6.054 -33.502 -20.415 0.49 35.28 ATOM 808 CA BCYS A 105 6.468 -34.015 -21.815 0.51 32.42 ATOM 809 CB BCYS A 105 6.025 -33.499 -20.452 0.51 35.38
If this is the case CPPTRAJ will print a warning about duplicate atom names but will take no other action. Both residues are considered ’CYS’ and the mask ’:CYS@CA’ would select both atom 806 and 809. Residue insertion codes are read in but also not used by the mask parser.
Charmm PSF:
[param ] [param <file>]
Read CHARMM parameters from given file. Can do multiple times.
Gromacs Top
By default CPPTRAJ will look for Gromacs topology data (that is not in the same directory) in the directory defined by the GMXDATA environment variable; specifically, it expects things to be in the “$GMXDATA/top” directory.