From 8d7b893b4d94029911986328b635be7478200dca Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 24 Apr 2017 14:03:49 +0200
Subject: [PATCH] Better doc molinfo
MOLTYPE is actually not needed in practice.
---
src/core/SetupMolInfo.cpp | 2 +-
src/setup/MolInfo.cpp | 7 ++++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/core/SetupMolInfo.cpp b/src/core/SetupMolInfo.cpp
index 662ddfb1c..ece94a7f0 100644
--- a/src/core/SetupMolInfo.cpp
+++ b/src/core/SetupMolInfo.cpp
@@ -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.");
}
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index c16a52207..03a0012f9 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -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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