a.m.u.). These listings are found in the {\tt atomtypes.atp}
file (.atp = {\bf a}tom {\bf t}ype {\bf p}arameter file).
Therefore, it is in this file that you can begin to change
-and/or add an atom type. A sample from the deprecated
-{\tt gmx.ff} force field is listed below.
+and/or add an atom type. A sample from the {\tt gromos43a1.ff}
+force field is listed below.
{\small
\begin{verbatim}
O 15.99940 ; carbonyl oxygen (C=O)
OM 15.99940 ; carboxyl oxygen (CO-)
- OA 15.99940 ; hydroxyl oxygen (OH)
+ OA 15.99940 ; hydroxyl, sugar or ester oxygen
OW 15.99940 ; water oxygen
N 14.00670 ; peptide nitrogen (N or NH)
NT 14.00670 ; terminal nitrogen (NH2)
NL 14.00670 ; terminal nitrogen (NH3)
- NR5 14.00670 ; aromatic N (5-ring,2 bonds)
- NR5* 14.00670 ; aromatic N (5-ring,3 bonds)
- NP 14.00670 ; porphyrin nitrogen
- C 12.01100 ; bare carbon (peptide,C=O,C-N)
- CH1 13.01900 ; aliphatic CH-group
- CH2 14.02700 ; aliphatic CH2-group
+ NR 14.00670 ; aromatic nitrogen
+ NZ 14.00670 ; Arg NH (NH2)
+ NE 14.00670 ; Arg NE (NH)
+ C 12.01100 ; bare carbon
+ CH1 13.01900 ; aliphatic or sugar CH-group
+ CH2 14.02700 ; aliphatic or sugar CH2-group
CH3 15.03500 ; aliphatic CH3-group
\end{verbatim}}
replaced by force field parameters by the C-preprocessor in {\tt grompp}
using {\tt \#define} statements.
-{\tt pdb2gmx} automatically generates all angles. This means that for the
-{\tt gmx.ff} force field,
-the {\tt [~angles~]} field is only useful for overriding {\tt .itp}
-parameters. For the \gromosv{96} force field the interaction number
-of all angles need to be specified.
+{\tt pdb2gmx} automatically generates all angles. This means that for
+most force fields the {\tt [~angles~]} field is only useful for overriding
+{\tt .itp} parameters. For the \gromosv{96} force field the interaction
+number of all angles needs to be specified.
{\tt pdb2gmx} automatically generates one proper dihedral for every rotatable
bond, preferably on heavy atoms. When the {\tt [~dihedrals~]} field is used,
{\tt aminoacids.c.tdb} for the N- and C-termini respectively. They contain
information for the {\tt pdb2gmx} program on how to connect new atoms
to existing ones, which atoms should be removed or changed, and which
-bonded interactions should be added. The format of the is as follows
-(from {\tt gmx.ff/aminoacids.c.tdb}):
+bonded interactions should be added. Their format is as follows
+(from {\tt gromos43a1.ff/aminoacids.c.tdb}):
{\small
\begin{verbatim}
-[ COO- ]
+[ None ]
+[ COO- ]
[ replace ]
-C C C 12.011 0.27
-
+C C C 12.011 0.27
+O O1 OM 15.9994 -0.635
+OXT O2 OM 15.9994 -0.635
[ add ]
-2 8 O C CA N
- OM 15.9994 -0.635
-
-[ delete ]
-O
-
+2 8 O C CA N
+ OM 15.9994 -0.635
+[ bonds ]
+C O1 gb_5
+C O2 gb_5
+[ angles ]
+O1 C O2 ga_37
+CA C O1 ga_21
+CA C O2 ga_21
+[ dihedrals ]
+N CA C O2 gd_20
[ impropers ]
-C O1 O2 CA
-
-[ None ]
+C CA O2 O1 gi_1
\end{verbatim}}
The file is organized in blocks, each with a header specifying the
{\tt \#include} statement followed by {\tt <name>.ff/forcefield.itp}.
This statement includes the force field file,
which, in turn, may include other force field files. All the force fields
-are organized in the same way. As an example, we show the {\tt gmx.ff/forcefield.itp}
+are organized in the same way. As an example, we show the {\tt gromos43a1.ff/forcefield.itp}
file:
{\small
\begin{verbatim}
-#define _FF_GROMACS
-#define _FF_GROMACS1
+#define _FF_GROMOS96
+#define _FF_GROMOS43A1
[ defaults ]
-; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
- 1 1 no 1.0 1.0
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+ 1 1 no 1.0 1.0
#include "ffnonbonded.itp"
#include "ffbonded.itp"
because all non-bonded parameters above the last {\tt [~atomtypes~]}
section would be overwritten using the standard combination rules.
-\section{{\tt gmx.ff} documentation}
-For backward compatibility we retain here some reference to parameters
-present in the {\tt gmx.ff} force field. The last 10 atom types were
-not part of the original \gromosv{87} force field~\cite{biomos}, so
-if you use them you should refer to one or more of the following
-papers:
-\begin{itemize}
-\item F was taken from ref.~\cite{Buuren93a},
-\item CP2 and CP3 from ref.~\cite{Buuren93b} and references cited therein,
-\item CR5, CR6 and HCR from ref.~\cite{Spoel96c}
-\item OWT3 from ref.~\cite{Jorgensen83}
-\item SD, OD and CD from ref.~\cite{Liu95}
-\end{itemize}
-{\bf Note that we recommend against using these parameters in new projects
-since they are not well-tested.}
-
% LocalWords: parameterized fffiles ptype polarizable gromacs atp ype arameter
% LocalWords: lll carboxyl OA hydroxyl NL porphyrin OPLS CP HCR OWT fd funct
% LocalWords: grompp statprop atomtype rtp esidue opology pdb gmx kJ mol gro
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff