Added reference to cmap in pdb2gmx.

Fixes #886.

Change-Id: Ib4c84a50962ed90ce145ad001322a9a46c8a2ab0

diff --git a/manual/forcefield.tex b/manual/forcefield.tex
index 1d35f33116a6a73e597ab59bcc61cf60e2ad38f0..9ffa55cc044a3b8c2d57b85424ffb9dc2aecf0f7 100644 (file)
--- a/manual/forcefield.tex
+++ b/manual/forcefield.tex
@@ -2898,6 +2898,7 @@ As of version 4.5, {\gromacs} provides native support for the following AMBER fo
 \end{itemize}
 
 \subsection{CHARMM\index{CHARMM force field}}
+\label{subsec:charmmff}
 
 As of version 4.5, {\gromacs} supports the CHARMM27 force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
 

diff --git a/manual/topology.tex b/manual/topology.tex
index c6f6fddc38676ce73e3925079f8cc140aff8d8c0..c5638116b5e48593c39062e7d4d3954b18dcacf2 100644 (file)
--- a/manual/topology.tex
+++ b/manual/topology.tex
@@ -737,7 +737,9 @@ number of all angles needs to be specified.
 bond, preferably on heavy atoms. When the {\tt [~dihedrals~]} field is used,
 no other dihedrals will be generated for the bonds corresponding to the
 specified  dihedrals. It is possible to put more than one dihedral
-function on a rotatable bond. 
+function on a rotatable bond. In the case of CHARMM27 FF {\tt pdb2gmx}
+can add correction maps to the dihedrals using the default {\tt -cmap} option.
+Please refer to \ssecref{charmmff} for more information.
 
 {\tt pdb2gmx} sets the number of exclusions to 3, which
 means that interactions between atoms connected by at most 3 bonds are