Action: MOLINFO
| Module | generic |
|---|---|
| Description | Usage |
| This command is used to provide information on the molecules that are present in your system. |   |
| This action outputs data to a file. You can read more about how PLUMED manages output files here |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| CHAIN | atoms | (for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure |
Further details and examples
This command is used to provide information on the molecules that are present in your system. A simple examples where this command is used to provide the information on which atoms are in the backbone of a protein to the ALPHARMSD action is shown below.
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#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=regtest/basic/rt32/helix.pdbClick here to see an extract from this file.ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=a
The following example prints the distance corresponding to the hydrogen bonds in a GC Watson-Crick pair.
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#SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=regtest/basic/rt-ermsd/ref.pdbClick here to see an extract from this file.MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=dna hb1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@N2-2the N2 atom in residue 2. Click here for more information. ,@O2-15the O2 atom in residue 15. Click here for more information. hb2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@N1-2the N1 atom in residue 2. Click here for more information. ,@N3-15the N3 atom in residue 15. Click here for more information. hb3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@O6-2the O6 atom in residue 2. Click here for more information. ,@N4-15the N4 atom in residue 15. Click here for more information. PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=hb1,hb2,hb3
The last example shows you how you can use MOLINFO to calculate torsion angles
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#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=regtest/basic/rt32/helix.pdbClick here to see an extract from this file.t1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. t2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1,t2 FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=10
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. Since the introduction of PLUMED 2.7 you have been able to use multiple MOLINFO actions. Every time you perform an atom selection, the last available MOLINFO action will be used. This allows you to provide multiple PDB files, for instance using different naming conventions (see issue 134).
[!CAUTION] 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 in the documentation for the PDB2CONSTANT command.
If the flag WHOLE is used, the reference structure is assumed to be whole, i.e. not broken by PBC.
This will impact PBC calculations in all the actions following the MOLINFO action!.
In particular, actions that reconstruct molecules locally will do the reconstruction using a
minimum spanning tree rather than the order in which atoms are provided.
Notice that in PLUMED 2.8, 2.9, and 2.10 this would only have affected the behavior of \ref WHOLEMOLECULES
actions, whereas starting with PLUMED 2.11 all actions that reconstruct PBCs are affected.
If you want a variable to ignore this, you can just repeate the MOLINFO action without
the WHOLE flag: all the following actions will use the traditional reconstruction algorithm,
based on the order in which atoms are listed.
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 keyword 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. All the various ways that the @ symbol can be used are listed in the following table:
In the table above you will find the following shortcuts that allow you to select atoms that are not part of 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)
[!CAUTION] Be careful since these choices are based on common names used in PDB files. Always check if the selected atoms are correct.
When you would like atoms from a specific residue you will use one of the atom selection commands from the above table with the following 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 you to select chains with a numeric id.
Breaking the table above down we see that for protein residues, the following groups are available:
# quadruplets for dihedral angles
@phi-#
@psi-#
@omega-#
@chi1-#
@chi2-#
@chi3-#
@chi4-#
@chi5-#
# all sidechain atoms (excluding glycine, including all hydrogens)
@sidechain-#
# all backbone atoms (including hydrogens)
@back-#
while 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 some shortcuts are available even when you not using the MOLINFO command.
[!CAUTION] If a residue-chain is repeated twice in the reference pdb only the first entry will be selected.
[!CAUTION] 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.
[!CAUTION] 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.
Advanced atom selection with mdtraj or MDAnalysis
Since PLUMED 2.6 it is possible to use the expressive selection syntax of mdtraj and/or MDAnalysis:
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#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=regtest/basic/rt32/helix.pdbClick here to see an extract from this file.PYTHON_BIN python interpreter=python g1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=@mda:atom selection built using syntax for MDAnalysis. Click here for more information. backbone g2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group={@mda:atom selection built using syntax for MDAnalysis. Click here for more information. {resnum 1 or resid 3:5}} g3: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group={@mda:atom selection built using syntax for MDAnalysis. Click here for more information. {resid 3:5} @mda:{resnum 1}} g4: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group={@mdt:atom selection built using syntax for mdtraj. Click here for more information. {protein and (backbone or resname ALA)}} g5: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group={@mdt:atom selection built using syntax for mdtraj. Click here for more information. {mass 5.5 to 20}} # masses guessed by mdtraj based on atom type! g6: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group={@mda:atom selection built using syntax for MDAnalysis. Click here for more information. {resid 3:5} 1-10 @mda:{resnum 1}the resid 3:5} 1 atom in residue 10 @mda:{resnum 1}. Click here for more information. }
Here @mda: indicates that the MDAnalysis language is used, whereas @mdt: indicates that the mdtraj language is used. Notice that these languages typically select atoms in order. If you want to specify a different order, you can chain definitions as in g3 above (compare with g2). Selections can be also chained with standard PLUMED selections (see g6).
The double braces are required due to the way PLUMED parses atom lists. In particular:
- The outer braces are needed to show PLUMED where the
ATOMS=...option ends. - The inner braces are needed to show PLUMED where each selector ends.
MDAnalysis also supports geometric selectors based on atomic coordinates. These selectors are static and return lists computed using the coordinates stored in the MOLINFO pdb file.
In order to use this syntax you should check the following points at runtime:
plumed --no-mpi config has subprocessprintssubprocess on(should be ok on most UNIX systems).- You have a python interpreter with mdtraj and/or MDAnalysis installed. You can check using:
python -c "import mdtraj"python -c "import MDAnalysis"
In order to install these packages refer to their documentation. Pip or conda install should be ok, provided you make sure the correct python interpreter is in the execution PATH at runtime. Notice that you will only need the package(s) related to the syntax that you want to use.
3. In case you installed these modules on a python with a different name (e.g. python3.6), the correct check is:
- python3.6 -c "import mdtraj"
- python3.6 -c "import MDAnalysis"
If this is the case, you should set the environment variable export PYTHON_BIN=python3.6 or export PLUMED_PYTHON_BIN=python3.6 (higher priority). Alternatively, directly provide the interpreter in the PLUMED input file
using MOLINFO PYTHON_BIN=python3.6 (even higher priority).
4. The PDB file that you provide to MOLINFO should have consecutive atom numbers starting from 1. This is currently enforced since reading atom numbers out of order (as PLUMED does) is not supported by other packages.
Advanced atom selection with VMD (experimental)
Similarly to the @mda: and @mdt: selectors above, you can use the two following selectors in order to
access to VMD syntax for atoms selection:
- @vmdexec:: This selector launches an instance of VMD, so vmd executable should be in your execution path.
Might be very slow or even crash your simulation. Notice that even if vmd executable is used,
the implementation is still python based and so a working python interpreter should be provided.
- @vmd:: This selector tries to import the vmd python module. Notice that the best way to obtain this module
is not within the standard VMD installer but rather by installing the python
module that can be found at this link.
The module is also available on conda.
You should make sure the module is available in the python interpreter used by MOLINFO
(check using the command python -c "import vmd").
These two selectors are experimental and might be removed at some point.
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| CHAIN | input | none | (for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure |
| STRUCTURE | compulsory | none | a file in pdb format containing a reference structure |
| MOLTYPE | compulsory | protein | what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible |
| PYTHON_BIN | compulsory | default | python interpreter |
| WHOLE | optional | false | The reference structure is whole, i |