table of contents
g_x2top(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_x2top(1) |
NAME¶
g_x2top - generates a primitive topology from coordinatesSYNOPSIS¶
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 realDESCRIPTION¶
g_x2top generates a primitive topology from a coordinate file. The program assumes all hydrogens are present when defining the hybridization 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.FILES¶
-f conf.gro InputStructure file: gro g96 pdb tpr etc.
Topology file
Residue Type file used by pdb2gmx
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
Force field for your simulation. Type "select" for interactive selection.
Generate verbose output in the top file.
Number of exclusions
Use 3rd neighbour interactions for hydrogen atoms
Generate all proper dihedrals
Remove dihedrals on the same bond as an improper
Output 1-4 interactions (pairs) in topology file
Name of your molecule
Use periodic boundary conditions.
Use the B-factor supplied in a .pdb file for the atomic charges
Print parameters in the output
Round off measured values
Bonded force constant (kJ/mol/nm2)
Angle force constant (kJ/mol/rad2)
Dihedral angle force constant (kJ/mol/rad2)
KNOWN PROBLEMS¶
- The atom type selection is primitive. Virtually no chemical knowledge is usedSEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |