diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp index 788d185d2fbbdd734f75dc2275e9c9df353a1d68..0c1679ee231b8c40ff1c009941be5bb8a69ccf8f 100644 --- a/src/setup/MolInfo.cpp +++ b/src/setup/MolInfo.cpp @@ -45,15 +45,28 @@ generated with `gmx editconf -f topol.tpr -o reference.pdb`. More information of the PDB parser implemented in PLUMED can be found \ref pdbreader "at this page". - -Using MOLINFO with a protein's or nucleic acid's pdb extends the possibility of atoms selection using the @ special -symbol. - 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 keyoword. +Using MOLINFO with a protein's or nucleic acid's pdb extends the possibility of atoms selection using the @ special +symbol in the form + +\verbatim +@"definition"-chainresiduenum +@"definition"-residuenum +\endverbatim + +So for example + +\verbatim +@psi-1 will select the atoms defining the psi torsion of residue 1 +@psi-C1 will define the same torsion for residue 1 of chain C. +\endverbatim + +In the following are listed the current available definitions: + For protein residues, the following groups are available: \verbatim @@ -101,9 +114,8 @@ For DNA or RNA residues, the following groups are available: 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. -If the chosen group name does not match any of the default ones, the parser looks for a single atom -with the same name. This means that it is also possible to pick single atoms using the syntax -`@atom-residue`. +Furthermore it is also possible to pick single atoms using the syntax +`@atom-chainresiduenum` or `@atom-residuenum`. \warning If a residue-chain is repeated twice in the reference pdb only the first entry will be selected. @@ -135,6 +147,14 @@ hb3: DISTANCE ATOMS=@O6-1,@N4-14 PRINT ARG=hb1,hb2,hb3 \endplumedfile +This example use MOLINFO to calculate torsions angles + +\verbatim +MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb +t1: TORSION ATOMS=@phi-3 +t2: TORSION ATOMS=@psi-4 +PRINT ARG=t1,t2 FILE=colvar STRIDE=10 +\endverbatim */ //+ENDPLUMEDOC diff --git a/user-doc/Group.md b/user-doc/Group.md index 3aa4d63d67c45590398bc7f730beaa6c6424519e..5472a030897205221a2a107fa02935d06a4c8cba 100644 --- a/user-doc/Group.md +++ b/user-doc/Group.md @@ -25,42 +25,6 @@ In addition, for certain colvars, pdb files can be read in using the following k @TOPOLOGY@ -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 using \ref MOLINFO. 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 commands where this has been implemented to specify atom lists. One place where this is -particularly useful is when using the commands \ref ALPHARMSD, \ref ANTIBETARMSD and \ref PARABETARMSD. - -MOLINFO also introduces special groups that can be used in atom selection. These special groups always begin with a \@ symbol. The -following special groups are currently available in PLUMED: - -<table align=center frame=void width=95%% cellpadding=5%%> -<tr> <td width=10%> <b> Symbol </b> </td> <td> <b> Topology type </b> </td> <td> <b> Despription </b> </td> </tr> -<tr> <td> \@phi-\# </td> <td> protein </td> <td> -The torsional angle defined by the C, CA, N and C atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot -</td> </tr> -<tr> <td> \@psi-\# </td> <td> protein </td> <td> -The torsional angle defined by the N, C, CA and N atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot -</td> </tr> -<tr> <td> \@omega-\# </td> <td> protein </td> <td> -The torsional angle defined by the CA, N, C and CA atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot -</td> </tr> -<tr> <td> \@chi1-\# </td> <td> protein </td> <td> -The first torsional angle of the sidechain of the \#th residue. Be aware that this angle is not defined for GLY or ALA residues. -See http://en.wikipedia.org/wiki/Ramachandran_plot -</td> </tr> -</table> - -The following example shows how to use \ref MOLINFO with \ref TORSION to calculate the torsion angles phi and psi for the first and fourth residue -of the protein: - -\plumedfile -MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb -t1: TORSION ATOMS=@phi-3 -t2: TORSION ATOMS=@psi-4 -PRINT ARG=t1,t2 FILE=colvar STRIDE=10 -\endplumedfile - \subsection pbc Broken Molecules and PBC PLUMED is designed so that for the majority of the CVs implemented the periodic boundary conditions are treated