This is part of the setup module

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.

Warning: 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 whenever you use the MOLINFO action. Also make sure that the atoms are listed in the pdb with the correct order. If you are using gromacs, the safest way is to use reference pdb file generated with gmx editconf -f topol.tpr -o reference.pdb.

More information of the PDB parser implemented in PLUMED can be found at this page.

Providing MOLTYPE=protein, MOLTYPE=rna, or MOLTYPE=dna will instruct plumed to look for known residues from these three types of molecule. In other words, this is available for historical reasons and to allow future extensions where alternative lists will be provided. As of now, you can just ignore this keyword.

Using MOLINFO extends the possibility of atoms selection using the @ special symbol. The following shortcuts are available that do not refer to one specific residue:

@nucleic : all atoms that are part of a DNA or RNA molecule
@protein : all atoms that are part of a protein
@water : all water molecules
@ions : all the ions
@hydrogens : all hydrogen atoms (those for which the first non-number in the name is a H)
@nonhydrogens : all non hydrogen atoms (those for which the first non-number in the name is not a H)

Warning: Be careful since these choices are based on common names used in PDB files. Always check if the selected atoms are correct.

In addition, atoms from a specific residue can be selected with a symbol in this form:

@"definition"-chain_residuenum
@"definition"-chainresiduenum
@"definition"-residuenum

So for example

@psi-1 will select the atoms defining the psi torsion of residue 1
@psi-C1  or @psi-C_1 will define the same torsion for residue 1 of chain C.
@psi-3_1 will define the same torsion for residue 1 of chain 3.

Using the underscore to separate chain and residue is available as of PLUMED 2.5 and allows selecting chains with a numeric id.

In the following are listed the current available definitions:

For protein residues, the following groups are available:

@phi-#
@psi-#
@omega-#
@chi1-#
@chi2-#
@chi3-#
@chi4-#
@chi5-#

that select the appropriate atoms that define each dihedral angle for residue #.

For DNA or RNA residues, the following groups are available:

# quadruplets for backbone dihedral angles
@alpha-#
@beta-#
@gamma-#
@delta-#
@epsilon-#
@zeta-#

# quadruplets for sugar dihedral angles
@v0-#
@v1-#
@v2-#
@v3-#
@v4-#

# quadruplet corresponding to the chi torsional angle
@chi-#

# backbone, sugar, and base heavy atoms
@back-#
@sugar-#
@base-#

# ordered triplets of atoms on the 6-membered ring of nucleobases
# namely:
#  C2/C4/C6 for pyrimidines
#  C2/C6/C4 for purines
@lcs-#

Notice that zeta and epsilon groups should not be used on 3' end residue and alpha and beta should not be used on 5' end residue.

Furthermore it is also possible to pick single atoms using the syntax atom-chain_residuenum, @atom-chainresiduenum or @atom-residuenum. As of PLUMED 2.5, this also works when the residue is not a protein/rna/dna residue. For instance, @OW-100 will select oxygen of water molecule with residue number 100.

Finally, notice that other shortcuts are available even when not using the MOLINFO command (see Specifying Atoms).

Warning: If a residue-chain is repeated twice in the reference pdb only the first entry will be selected.

Bug:: At the moment the HA1 atoms in a GLY residues are treated as if they are the CB atoms. This may or may not be true - GLY is problematic for secondary structure residues as it is achiral.

Bug:: If you use WHOLEMOLECULES RESIDUES=1-10 for a 18 amino acid protein ( 18 amino acids + 2 terminal groups = 20 residues ) the code will fail as it will not be able to interpret terminal residue 1.

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.. For more information on how to specify lists of atoms see Groups and Virtual Atoms

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
MOLTYPE	( default=protein ) what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible

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.

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=reference.pdb
ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a

The following example prints the distance corresponding to the hydrogen bonds in a GC Watson-Crick pair.

#SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb
MOLINFO STRUCTURE=reference.pdb MOLTYPE=dna
hb1: DISTANCE ATOMS=@N2-2,@O2-15
hb2: DISTANCE ATOMS=@N1-2,@N3-15
hb3: DISTANCE ATOMS=@O6-2,@N4-15
PRINT ARG=hb1,hb2,hb3

This example use MOLINFO to calculate torsion angles

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=10