MOLINFO

This command is used to provide information on the molecules that are present in your system.

The information on the molecules in your system can either be provided in the form of a pdb file or as a set of lists of atoms that describe the various chains in your system. If a pdb file is used plumed the MOLINFO command will endeavor to recognize the various chains and residues that make up the molecules in your system using the chainIDs and resnumbers from the pdb file. You can then use this information in later commands to specify atom lists in terms residues. For example using this command you can find the backbone atoms in your structure automatically.

Please be aware that the pdb parser in plumed is far from perfect. You should thus check the log file and examine what plumed is actually doing whenenver you use the MOLINFO action.

Bug:

At the moment all atoms named HA1 are treated as if they are CB atoms. This makes it possible to deal with GLY residues in colvars like ALPHARMSD.

The atoms involved can be specified using

CHAIN

(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure.

Compulsory keywords

STRUCTURE

a file in pdb format containing a reference structure. This is used to defines the atoms in the various residues, chains, etc . For more details on the PDB file format visit http://www.wwpdb.org/docs.html

Examples

In the following example the MOLINFO command is used to provide the information on which atoms are in the backbone of a protein to the ALPHARMSD CV.

MOLINFO STRUCTURE=reference.pdb
ALPHARMSD BACKBONE=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a

(see also ALPHARMSD)