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Commit 8d7b893b authored by Giovanni Bussi's avatar Giovanni Bussi
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Better doc molinfo

MOLTYPE is actually not needed in practice.
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......@@ -43,7 +43,7 @@ void SetupMolInfo::registerKeywords( Keywords& keys ) {
keys.add("compulsory","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");
keys.add("compulsory","MOLTYPE","protein","what kind of molecule is contained in the pdb file");
keys.add("compulsory","MOLTYPE","protein","what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible");
keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure.");
}
......
......@@ -44,12 +44,13 @@ If you are using gromacs, the safest way is to use reference pdb file
generated with `gmx editconf -f topol.tpr -o reference.pdb`.
Using MOLINFO with a protein's pdb extend the possibility of atoms selection using the @ special
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 (so that any of these three choice
can be safely used in a RNA/protein complex).
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.
For protein residues, the following groups are available:
......
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