CP2 CP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
\end{verbatim}}
-%Also in this file are the
-%\normindex{Ryckaert-Bellemans}~\cite{Ryckaert78} parameters for the
-%CP2-CP2 dihedrals in alkanes or alkane tails with the following
-%constants:
-
-%\begin{center}
-%(kJ/mol)\\
-%\begin{tabular}{llrllrllr}
-%$C_0$ & $=$ & $~ 9.28$ & $C_2$ & $=$ & $-13.12$ & $C_4$ & $=$ & $ 26.24$ \\
-%$C_1$ & $=$ & $ 12.16$ & $C_3$ & $=$ & $~-3.06$ & $C_5$ & $=$ & $-31.5 $ \\
-%\end{tabular}
-%\end{center}
-
-%({\bf Note:} The use of this potential implies the exclusion of LJ interactions
-%between the first and the last atom of the dihedral, and $\psi$ is defined
-%according to the ``\swapindex{polymer}{convention}'' ($\psi_{trans}=0$)).
-
-%So there are three types of dihedrals in the {\gromacs} force field:
-%\begin{itemize}
-%\item \swapindex{proper}{dihedral} : funct = 1, with mult = multiplicity, so the
-% number of possible angles
-%\item \swapindex{improper}{dihedral} : funct = 2
-%\item Ryckaert-Bellemans dihedral : funct = 3
-%\end{itemize}
-
In the {\tt ffbonded.itp} file, you can add bonded parameters. If you
want to include parameters for new atom types, make sure you define
them in {\tt atomtypes.atp} as well.
; Example topology file
;
; The force field files to be included
-#include "gmx.ff/forcefield.itp"
+#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name nrexcl
Urea 3
[ atoms ]
-; nr type resnr residu atom cgnr charge
- 1 C 1 UREA C1 1 0.683
- 2 O 1 UREA O2 1 -0.683
- 3 NT 1 UREA N3 2 -0.622
- 4 H 1 UREA H4 2 0.346
- 5 H 1 UREA H5 2 0.276
- 6 NT 1 UREA N6 3 -0.622
- 7 H 1 UREA H7 3 0.346
- 8 H 1 UREA H8 3 0.276
+ 1 C 1 URE C 1 0.880229 12.01000 ; amber C type
+ 2 O 1 URE O 2 -0.613359 16.00000 ; amber O type
+ 3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type
+ 4 H 1 URE H11 4 0.395055 1.00800 ; amber H type
+ 5 H 1 URE H12 5 0.395055 1.00800 ; amber H type
+ 6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type
+ 7 H 1 URE H21 7 0.395055 1.00800 ; amber H type
+ 8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
-; ai aj funct b0 kb
- 3 4 1 1.000000e-01 3.744680e+05
- 3 5 1 1.000000e-01 3.744680e+05
- 6 7 1 1.000000e-01 3.744680e+05
- 6 8 1 1.000000e-01 3.744680e+05
- 1 2 1 1.230000e-01 5.020800e+05
- 1 3 1 1.330000e-01 3.765600e+05
- 1 6 1 1.330000e-01 3.765600e+05
-
-[ pairs ]
-; ai aj funct c6 c12
- 2 4 1 0.000000e+00 0.000000e+00
- 2 5 1 0.000000e+00 0.000000e+00
- 2 7 1 0.000000e+00 0.000000e+00
- 2 8 1 0.000000e+00 0.000000e+00
- 3 7 1 0.000000e+00 0.000000e+00
- 3 8 1 0.000000e+00 0.000000e+00
- 4 6 1 0.000000e+00 0.000000e+00
- 5 6 1 0.000000e+00 0.000000e+00
-
-[ angles ]
-; ai aj ak funct th0 cth
- 1 3 4 1 1.200000e+02 2.928800e+02
- 1 3 5 1 1.200000e+02 2.928800e+02
- 4 3 5 1 1.200000e+02 3.347200e+02
- 1 6 7 1 1.200000e+02 2.928800e+02
- 1 6 8 1 1.200000e+02 2.928800e+02
- 7 6 8 1 1.200000e+02 3.347200e+02
- 2 1 3 1 1.215000e+02 5.020800e+02
- 2 1 6 1 1.215000e+02 5.020800e+02
- 3 1 6 1 1.170000e+02 5.020800e+02
-
-[ dihedrals ]
-; ai aj ak al funct phi cp mult
- 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
- 6 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
- 2 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
- 6 1 3 5 1 1.800000e+02 3.347200e+01 2.000000e+00
- 2 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
- 3 1 6 7 1 1.800000e+02 3.347200e+01 2.000000e+00
- 2 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
- 3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
-
-[ dihedrals ]
-; ai aj ak al funct q0 cq
- 3 4 5 1 2 0.000000e+00 1.673600e+02
- 6 7 8 1 2 0.000000e+00 1.673600e+02
- 1 3 6 2 2 0.000000e+00 1.673600e+02
+ 1 2
+ 1 3
+ 1 6
+ 3 4
+ 3 5
+ 6 7
+ 6 8
+
+[ dihedrals ]
+; ai aj ak al funct definition
+ 2 1 3 4 9
+ 2 1 3 5 9
+ 2 1 6 7 9
+ 2 1 6 8 9
+ 3 1 6 7 9
+ 3 1 6 8 9
+ 6 1 3 4 9
+ 6 1 3 5 9
+
+[ dihedrals ]
+ 3 6 1 2 4
+ 1 4 3 5 4
+ 1 7 6 8 4
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
2 1 1000 0 1000 ; Restrain to a line (Y-axis)
3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
-; Include SPC water topology
-#include "spc.itp"
+; Include TIP3P water topology
+#include "amber99/tip3p.itp"
[ system ]
Urea in Water
Here follows the explanatory text.
+{\bf {\tt \#include "amber99.ff/forcefield.itp"} :} this includes the
+information for the force field you are using, including
+bonded and non-bonded parameters. This example uses the AMBER99 force
+field, but your simulation may use a different force field.
+{\tt grompp} will automatically go and find this file and copy-and-paste
+its content. That content can be seen in
+\linebreak {\tt share/top/amber99.ff/forcefield.itp}, and it is
+
+{\small
+\begin{verbatim}
+#define _FF_AMBER
+#define _FF_AMBER99
+
+[ defaults ]
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
+1 2 yes 0.5 0.8333
+
+#include "ffnonbonded.itp"
+#include "ffbonded.itp"
+#include "gbsa.itp"
+\end{verbatim}}
+
+The two {\tt \#define} statements set up the conditions so that
+future parts of the topology can know that the AMBER 99 force
+field is in use.
+
{\bf {\tt [~defaults~]} :}
\begin{itemize}
\item {\tt nbfunc} is the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham)
{\tt fudgeQQ} is always used. However, if you
want to specify $N$ you need to give a value for the other parameters as well.
+Then some other {\tt \#include} statements add in the large amount of data needed
+to describe the rest of the force field. We will skip these and return to {\tt urea.top}.
+There we will see
+
% move these figures so they end up on facing pages
% (first figure on even page)
%\input{topolfig}
-{\bf {\tt \#include "gmx.ff/forcefield.itp"} :} this includes the bonded and
-non-bonded force field parameters, the {\tt gmx} in {\tt gmx.ff} will be
-replaced by the name of the force field you are actually using.
-
{\bf {\tt [~moleculetype~]} :} defines the name of your molecule in
this {\tt *.top} and nrexcl = 3 stands for excluding non-bonded
interactions between atoms that are no further than 3 bonds away.
{\bf {\tt [~angles~]} :} no comment
{\bf {\tt [~dihedrals~]} :} in this case there are 9 proper dihedrals
-(funct = 1), 3 improper (funct = 2) and no Ryckaert-Bellemans type
+(funct = 1), 3 improper (funct = 4) and no Ryckaert-Bellemans type
dihedrals. If you want to include Ryckaert-Bellemans type dihedrals
in a topology, do the following (in case of {\eg} decane):
\begin{verbatim}
The reference positions are read from a
separate coordinate file by {\tt \normindex{grompp}}.
-{\bf {\tt \#include "spc.itp"} :} includes a topology file that was already
+{\bf {\tt \#include "tip3p.itp"} :} includes a topology file that was already
constructed (see section~\ssecref{molitp}).
{\bf {\tt [~system~]} :} title of your system, user-defined
{\bf {\tt [~molecules~]} :} this defines the total number of (sub)molecules
in your system that are defined in this {\tt *.top}. In this
example file, it stands for 1 urea molecule dissolved in 1000 water
-molecules. The molecule type SOL is defined in the {\tt spc.itp} file.
+molecules. The molecule type SOL is defined in the {\tt tip3p.itp} file.
Each name here must correspond to a name given with {\tt [~moleculetype~]}
earlier in the topology. The order of the blocks of molecule types and
the numbers of such molecules must match the coordinate file that
\subsection{Molecule.itp file}
\label{subsec:molitp}
If you construct a topology file you will use frequently (like the water
-molecule, {\tt spc.itp}, which is already constructed for you) it is
+molecule, {\tt tip3p.itp}, which is already constructed for you) it is
good to make a {\tt molecule.itp} file. This only lists the
information of one particular molecule and allows you to re-use the
{\tt [ moleculetype ]} in multiple systems without re-invoking
-{\tt pdb2gmx} or manually copying and pasting. An example follows:
+{\tt pdb2gmx} or manually copying and pasting. An example
+{\tt urea.itp} follows:
{\small
\begin{verbatim}
[ moleculetype ]
-; name nrexcl
-Urea 3
+; molname nrexcl
+URE 3
[ atoms ]
-; nr type resnr residu atom cgnr charge
- 1 C 1 UREA C1 1 0.683
- .................
- .................
- 8 H 1 UREA H8 3 0.276
+ 1 C 1 URE C 1 0.880229 12.01000 ; amber C type
+...
+ 8 H 1 URE H22 8 0.395055 1.00800 ; amber H type
[ bonds ]
-; ai aj funct c0 c1
- 3 4 1 1.000000e-01 3.744680e+05
- .................
- .................
- 1 6 1 1.330000e-01 3.765600e+05
-
-[ pairs ]
-; ai aj funct c0 c1
- 2 4 1 0.000000e+00 0.000000e+00
- .................
- .................
- 5 6 1 0.000000e+00 0.000000e+00
-
-[ angles ]
-; ai aj ak funct c0 c1
- 1 3 4 1 1.200000e+02 2.928800e+02
- .................
- .................
- 3 1 6 1 1.170000e+02 5.020800e+02
-
-[ dihedrals ]
-; ai aj ak al funct c0 c1 c2
- 2 1 3 4 1 1.800000e+02 3.347200e+01 2.000000e+00
- .................
- .................
- 3 1 6 8 1 1.800000e+02 3.347200e+01 2.000000e+00
-
-[ dihedrals ]
-; ai aj ak al funct c0 c1
- 3 4 5 1 2 0.000000e+00 1.673600e+02
- 6 7 8 1 2 0.000000e+00 1.673600e+02
- 1 3 6 2 2 0.000000e+00 1.673600e+02
+ 1 2
+...
+ 6 8
+[ dihedrals ]
+; ai aj ak al funct definition
+ 2 1 3 4 9
+...
+ 6 1 3 5 9
+[ dihedrals ]
+ 3 6 1 2 4
+ 1 4 3 5 4
+ 1 7 6 8 4
\end{verbatim}}
Using {\tt *.itp} files results in a very short {\tt *.top} file:
{\small
\begin{verbatim}
+;
+; Example topology file
+;
; The force field files to be included
-#include "gmx.ff/forcefield.itp"
-
-; Include urea topology
+#include "amber99.ff/forcefield.itp"
+
#include "urea.itp"
-; Include SPC water topology
-#include "spc.itp"
+; Include TIP3P water topology
+#include "amber99/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
-;molecule name number
-Urea 1
-SOL 1000
+;molecule name nr.
+Urea 1
+SOL 1000
\end{verbatim}}
\subsection{Ifdef statements}
\label{subsec:ifdef}
A very powerful feature in {\gromacs} is the use of {\tt \#ifdef}
statements in your {\tt *.top} file. By making use of this statement,
+and associated {\tt \#define} statements like were seen in
+\linebreak {\tt amber99.ff/forcefield.itp} earlier,
different parameters for one molecule can be used in the same
{\tt *.top} file. An example is given for TFE, where there is an option to
use different charges on the atoms: charges derived by De Loof
; ai aj funct length_A length_B
1 2 2 0.7 1.7
-#include "spc.itp"
+#include "gromos43a1.ff/spc.itp"
[ system ]
; Name
\subsection{Force field files}
\label{subsec:fffiles}
-As of {\gromacs} version 4.5, 14 force fields are available by default.
+Many force fields are available by default.
Force fields are detected by the presence of {\tt <name>.ff} directories
in the {\gromacs} {\tt /share/top} sub-directory and/or the working directory.
The information regarding the location of the force field files is printed
{\small
\begin{itemize}
- \item AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
- \item AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
- \item AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
- \item AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
- \item AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
- \item AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
- \item AMBERGS force field (Garcia \& Sanbonmatsu, PNAS 99, 2782-2787, 2002)
- \item CHARMM27 all-atom force field (with CMAP)
- \item GROMOS96 43A1 force field
- \item GROMOS96 43A2 force field (improved alkane dihedrals)
- \item GROMOS96 45A3 force field (Schuler JCC 2001 22 1205)
- \item GROMOS96 53A5 force field (JCC 2004 vol 25 pag 1656)
- \item GROMOS96 53A6 force field (JCC 2004 vol 25 pag 1656)
- \item OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
+ \item AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
+ \item AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
+ \item AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
+ \item AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
+ \item AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
+ \item AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
+ \item AMBER99SB-ILDN-BSC0 protein, nucleic AMBER94 with ParmBSC0 (Perez et al., Biophys J. 2, 3817–29, 2007)
+ \item AMBERGS force field (Garcia \& Sanbonmatsu, PNAS 99, 2782-2787, 2002)
+ \item CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
+ \item GROMOS96 43a1 force field
+ \item GROMOS96 43a2 force field (improved alkane dihedrals)
+ \item GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
+ \item GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
+ \item GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
+ \item GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
+ \item OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
\end{itemize}}
-There are also some additional deprecated force fields listed in the selection from
-{\tt pdb2gmx}, but we do not currently recommend that you use those for new simulations.
-
A force field is included at the beginning of a topology file with an
{\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 gromos43a1.ff/forcefield.itp}
-file:
-
-{\small
-\begin{verbatim}
-#define _FF_GROMOS96
-#define _FF_GROMOS43A1
-
-[ defaults ]
-; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
- 1 1 no 1.0 1.0
-
-#include "ffnonbonded.itp"
-#include "ffbonded.itp"
-\end{verbatim}}
-
-The first {\tt \#define} can be used in topologies to parse data which is
-specific for all {\gromacs} force fields, the second {\tt \#define} is to parse
-data specific to this force field. The {\tt [~defaults~]} section is
-explained in \ssecref{topfile}. The included file {\tt ffnonbonded.itp} contains
-all atom types and non-bonded parameters. The included file {\tt ffbonded.itp}
-contains all bonded parameters.
+are organized in the same way. An example of the
+{\tt amber99.ff/forcefield.itp} was shown in \ssecref{topfile}.
For each force field, there several files which are only used by {\tt pdb2gmx}.
These are: residue databases ({\tt .rtp}, see~\ssecref{rtp})
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff