performed using the GROMACS software and the CHARMM22*
force field [46] and its trajectory was available in the XTC file
format (see Note 2 for details on compatibility with trajectory
formats). The steps described below were carried out on a server
running Ubuntu Server 14.04 from the command line, or on a
common MacBook Pro running macOS when a graphical user
interface was required, as when using xPyder.
3 Methods
3.1 Preparation
of Topology
and Trajectory
for the Analysis
As most trajectory analysis tools, PyInteraph requires a topology
and a trajectory file to work (see Notes 2 and 3). As the software
relies on atom names to recognize different analysis groups, the
names in the topology file should be consistent with atom and
group definitions that the software uses, so that PyInteraph can
correctly recognize the groups between which interactions are
calculated. This means that the user can either modify the configuration file so that it matches the definitions in the topology file or,
conversely, modify the topology file so that atom names match the
definition in the configuration files. It should be noted that the
latter uses standard PDB residue and atom names, meaning that
they should fit most cases (see Note 4 for more details on analysis
customization). Nonetheless, depending on the setup of each simulation and used software, some adjustments may be required, as
MD software frequently assign non-standard names to residues or
atoms depending on the force-field definition. Running pyinteraph
with the verbose option (Àv) outputs the groups from the topology
that the program will use for calculation, meaning that the user can
always verify whether the program recognizes groups correctly. In
particular:
1. For hydrophobic interactions, no adjustment is usually necessary. Nonetheless, when asking the software to use force-field
masses during calculation (option --ff-masses of the pyinteraph
executable), masses will be assigned according to residue and
atom names. Standard atom and residue names are required to
assign masses correctly, and the software will try to guess the
element corresponding to the atom type and to assign a mass
value accordingly if they are not already available. This is especially important for force fields that use non-standard masses
for heavy atoms (as united-atoms or coarse-grained force fields;
see details in Note 5).
2. For hydrogen bonds, no adjustment is necessary in case the
topology file uses standard atom names.
3. For charged groups, no adjustment is necessary in case the
topology file uses standard atom names and standard residue
names.
Interaction Networks with PyInteraph
159
force field [46] and its trajectory was available in the XTC file
format (see Note 2 for details on compatibility with trajectory
formats). The steps described below were carried out on a server
running Ubuntu Server 14.04 from the command line, or on a
common MacBook Pro running macOS when a graphical user
interface was required, as when using xPyder.
3 Methods
3.1 Preparation
of Topology
and Trajectory
for the Analysis
As most trajectory analysis tools, PyInteraph requires a topology
and a trajectory file to work (see Notes 2 and 3). As the software
relies on atom names to recognize different analysis groups, the
names in the topology file should be consistent with atom and
group definitions that the software uses, so that PyInteraph can
correctly recognize the groups between which interactions are
calculated. This means that the user can either modify the configuration file so that it matches the definitions in the topology file or,
conversely, modify the topology file so that atom names match the
definition in the configuration files. It should be noted that the
latter uses standard PDB residue and atom names, meaning that
they should fit most cases (see Note 4 for more details on analysis
customization). Nonetheless, depending on the setup of each simulation and used software, some adjustments may be required, as
MD software frequently assign non-standard names to residues or
atoms depending on the force-field definition. Running pyinteraph
with the verbose option (Àv) outputs the groups from the topology
that the program will use for calculation, meaning that the user can
always verify whether the program recognizes groups correctly. In
particular:
1. For hydrophobic interactions, no adjustment is usually necessary. Nonetheless, when asking the software to use force-field
masses during calculation (option --ff-masses of the pyinteraph
executable), masses will be assigned according to residue and
atom names. Standard atom and residue names are required to
assign masses correctly, and the software will try to guess the
element corresponding to the atom type and to assign a mass
value accordingly if they are not already available. This is especially important for force fields that use non-standard masses
for heavy atoms (as united-atoms or coarse-grained force fields;
see details in Note 5).
2. For hydrogen bonds, no adjustment is necessary in case the
topology file uses standard atom names.
3. For charged groups, no adjustment is necessary in case the
topology file uses standard atom names and standard residue
names.
Interaction Networks with PyInteraph
159