g_x2top(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_x2top(1)NAME
g_x2top - generates a primitive topology from coordinates
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_x2top -f conf.gro -o out.top -r out.rtp -[no]h -[no]version -nice int -ff string -[no]v -nexcl int -[no]H14 -[no]alldih -[no]remdih
-[no]pairs -name string -[no]pbc -[no]pdbq -[no]param -[no]round -kb real -kt real -kp real
DESCRIPTION
g_x2top generates a primitive topology from a coordinate file. The program assumes all hydrogens are present when defining the hybridiza-
tion from the atom name and the number of bonds. The program can also make an .rtp entry, which you can then add to the .rtp database.
When -param is set, equilibrium distances and angles and force constants will be printed in the topology for all interactions. The equi-
librium distances and angles are taken from the input coordinates, the force constant are set with command line options. The force fields
somewhat supported currently are:
G53a5 GROMOS96 53a5 Forcefield (official distribution)
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
The corresponding data files can be found in the library directory with name atomname2type.n2t. Check Chapter 5 of the manual for more
information about file formats. By default, the force field selection is interactive, but you can use the -ff option to specify one of the
short names above on the command line instead. In that case g_x2top just looks for the corresponding file.
FILES -f conf.gro Input
Structure file: gro g96 pdb tpr etc.
-o out.top Output, Opt.
Topology file
-r out.rtp Output, Opt.
Residue Type file used by pdb2gmx
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-ff string oplsaa
Force field for your simulation. Type "select" for interactive selection.
-[no]vno
Generate verbose output in the top file.
-nexcl int 3
Number of exclusions
-[no]H14yes
Use 3rd neighbour interactions for hydrogen atoms
-[no]alldihno
Generate all proper dihedrals
-[no]remdihno
Remove dihedrals on the same bond as an improper
-[no]pairsyes
Output 1-4 interactions (pairs) in topology file
-name string ICE
Name of your molecule
-[no]pbcyes
Use periodic boundary conditions.
-[no]pdbqno
Use the B-factor supplied in a .pdb file for the atomic charges
-[no]paramyes
Print parameters in the output
-[no]roundyes
Round off measured values
-kb real 400000
Bonded force constant (kJ/mol/nm2)
-kt real 400
Angle force constant (kJ/mol/rad2)
-kp real 5
Dihedral angle force constant (kJ/mol/rad2)
KNOWN PROBLEMS
- The atom type selection is primitive. Virtually no chemical knowledge is used
- Periodic boundary conditions screw up the bonding
- No improper dihedrals are generated
- The atoms to atomtype translation table is incomplete ( atomname2type.n2t file in the data directory). Please extend it and send the
results back to the GROMACS crew.
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_x2top(1)
Check Out this Related Man Page
grompp(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c grompp(1)NAME
grompp - makes a run input file
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
grompp -f grompp.mdp -po mdout.mdp -c conf.gro -r conf.gro -rb conf.gro -n index.ndx -p topol.top -pp processed.top -o topol.tpr -t
traj.trr -e ener.edr -[no]h -[no]version -nice int -[no]v -time real -[no]rmvsbds -maxwarn int -[no]zero -[no]renum
DESCRIPTION
The gromacs preprocessor reads a molecular topology file, checks the validity of the file, expands the topology from a molecular descrip-
tion to an atomic description. The topology file contains information about molecule types and the number of molecules, the preprocessor
copies each molecule as needed. There is no limitation on the number of molecule types. Bonds and bond-angles can be converted into con-
straints, separately for hydrogens and heavy atoms. Then a coordinate file is read and velocities can be generated from a Maxwellian dis-
tribution if requested. grompp also reads parameters for the mdrun (eg. number of MD steps, time step, cut-off), and others such as NEMD
parameters, which are corrected so that the net acceleration is zero. Eventually a binary file is produced that can serve as the sole
input file for the MD program.
grompp uses the atom names from the topology file. The atom names in the coordinate file (option -c) are only read to generate warnings
when they do not match the atom names in the topology. Note that the atom names are irrelevant for the simulation as only the atom types
are used for generating interaction parameters.
grompp uses a built-in preprocessor to resolve includes, macros, etc. The preprocessor supports the following keywords:
ifdef VARIABLE
ifndef VARIABLE
else
endif
define VARIABLE
undef VARIABLE include "filename"
include filename
The functioning of these statements in your topology may be modulated by using the following two flags in your .mdp file:
define = -DVARIABLE1 -DVARIABLE2
include = -I/home/john/doe
For further information a C-programming textbook may help you out. Specifying the -pp flag will get the pre-processed topology file writ-
ten out so that you can verify its contents.
When using position restraints a file with restraint coordinates can be supplied with -r, otherwise restraining will be done with respect
to the conformation from the -c option. For free energy calculation the the coordinates for the B topology can be supplied with -rb,
otherwise they will be equal to those of the A topology.
Starting coordinates can be read from trajectory with -t. The last frame with coordinates and velocities will be read, unless the -time
option is used. Only if this information is absent will the coordinates in the -c file be used. Note that these velocities will not be
used when gen_vel = yes in your .mdp file. An energy file can be supplied with -e to read Nose-Hoover and/or Parrinello-Rahman coupling
variables.
grompp can be used to restart simulations (preserving continuity) by supplying just a checkpoint file with -t. However, for simply
changing the number of run steps to extend a run, using tpbconv is more convenient than grompp. You then supply the old checkpoint file
directly to mdrun with -cpi. If you wish to change the ensemble or things like output frequency, then supplying the checkpoint file to
grompp with -t along with a new .mdp file with -f is the recommended procedure.
By default, all bonded interactions which have constant energy due to virtual site constructions will be removed. If this constant energy
is not zero, this will result in a shift in the total energy. All bonded interactions can be kept by turning off -rmvsbds. Additionally,
all constraints for distances which will be constant anyway because of virtual site constructions will be removed. If any constraints
remain which involve virtual sites, a fatal error will result.
To verify your run input file, please take note of all warnings on the screen, and correct where necessary. Do also look at the contents of
the mdout.mdp file; this contains comment lines, as well as the input that grompp has read. If in doubt, you can start grompp with the
-debug option which will give you more information in a file called grompp.log (along with real debug info). You can see the contents of
the run input file with the gmxdump program. gmxcheck can be used to compare the contents of two run input files.
The -maxwarn option can be used to override warnings printed by grompp that otherwise halt output. In some cases, warnings are harmless,
but usually they are not. The user is advised to carefully interpret the output messages before attempting to bypass them with this option.
FILES -f grompp.mdp Input
grompp input file with MD parameters
-po mdout.mdp Output
grompp input file with MD parameters
-c conf.gro Input
Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt.
Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt.
Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt.
Index file
-p topol.top Input
Topology file
-pp processed.top Output, Opt.
Topology file
-o topol.tpr Output
Run input file: tpr tpb tpa
-t traj.trr Input, Opt.
Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt.
Energy file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-[no]vno
Be loud and noisy
-time real -1
Take frame at or first after this time.
-[no]rmvsbdsyes
Remove constant bonded interactions with virtual sites
-maxwarn int 0
Number of allowed warnings during input processing. Not for normal use and may generate unstable systems
-[no]zerono
Set parameters for bonded interactions without defaults to zero instead of generating an error
-[no]renumyes
Renumber atomtypes and minimize number of atomtypes
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 grompp(1)