1GMX-EDITCONF(1) GROMACS GMX-EDITCONF(1)
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6 gmx-editconf - Convert and manipulates structure files
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9 gmx editconf [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-bf [<.dat>]]
10 [-o [<.gro/.g96/...>]] [-mead [<.pqr>]] [-[no]w]
11 [-[no]ndef] [-bt <enum>] [-box <vector>]
12 [-angles <vector>] [-d <real>] [-[no]c]
13 [-center <vector>] [-aligncenter <vector>]
14 [-align <vector>] [-translate <vector>]
15 [-rotate <vector>] [-[no]princ] [-scale <vector>]
16 [-density <real>] [-[no]pbc] [-resnr <int>] [-[no]grasp]
17 [-rvdw <real>] [-[no]sig56] [-[no]vdwread] [-[no]atom]
18 [-[no]legend] [-label <string>] [-[no]conect]
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21 gmx editconf converts generic structure format to .gro, .g96 or .pdb.
22 The box can be modified with options -box, -d and -angles. Both -box
24 and -d will center the system in the box, unless -noc is used. The
25 -center option can be used to shift the geometric center of the system
26 from the default of (x/2, y/2, z/2) implied by -c to some other value.
27 Option -bt determines the box type: triclinic is a triclinic box, cubic
29 is a rectangular box with all sides equal dodecahedron represents a
30 rhombic dodecahedron and octahedron is a truncated octahedron. The
31 last two are special cases of a triclinic box. The length of the three
32 box vectors of the truncated octahedron is the shortest distance
33 between two opposite hexagons. Relative to a cubic box with some peri‐
34 odic image distance, the volume of a dodecahedron with this same peri‐
35 odic distance is 0.71 times that of the cube, and that of a truncated
36 octahedron is 0.77 times.
37 Option -box requires only one value for a cubic, rhombic dodecahedral,
39 or truncated octahedral box.
40 With -d and a triclinic box the size of the system in the x-, y-, and
42 z-directions is used. With -d and cubic, dodecahedron or octahedron
43 boxes, the dimensions are set to the diameter of the system (largest
44 distance between atoms) plus twice the specified distance.
45 Option -angles is only meaningful with option -box and a triclinic box
47 and cannot be used with option -d.
48 When -n or -ndef is set, a group can be selected for calculating the
50 size and the geometric center, otherwise the whole system is used.
51 -rotate rotates the coordinates and velocities.
53 -princ aligns the principal axes of the system along the coordinate
55 axes, with the longest axis aligned with the x-axis. This may allow
56 you to decrease the box volume, but beware that molecules can rotate
57 significantly in a nanosecond.
58 Scaling is applied before any of the other operations are performed.
60 Boxes and coordinates can be scaled to give a certain density (option
61 -density). Note that this may be inaccurate in case a .gro file is
62 given as input. A special feature of the scaling option is that when
63 the factor -1 is given in one dimension, one obtains a mirror image,
64 mirrored in one of the planes. When one uses -1 in three dimensions, a
65 point-mirror image is obtained.
66 Groups are selected after all operations have been applied.
68 Periodicity can be removed in a crude manner. It is important that the
70 box vectors at the bottom of your input file are correct when the peri‐
71 odicity is to be removed.
72 When writing .pdb files, B-factors can be added with the -bf option.
74 B-factors are read from a file with with following format: first line
75 states number of entries in the file, next lines state an index fol‐
76 lowed by a B-factor. The B-factors will be attached per residue unless
77 the number of B-factors is larger than the number of the residues or
78 unless the -atom option is set. Obviously, any type of numeric data can
79 be added instead of B-factors. -legend will produce a row of CA atoms
80 with B-factors ranging from the minimum to the maximum value found,
81 effectively making a legend for viewing.
82 With the option -mead a special .pdb (.pqr) file for the MEAD electro‐
84 statics program (Poisson-Boltzmann solver) can be made. A further pre‐
85 requisite is that the input file is a run input file. The B-factor
86 field is then filled with the Van der Waals radius of the atoms while
87 the occupancy field will hold the charge.
88 The option -grasp is similar, but it puts the charges in the B-factor
90 and the radius in the occupancy.
91 Option -align allows alignment of the principal axis of a specified
93 group against the given vector, with an optional center of rotation
94 specified by -aligncenter.
95 Finally, with option -label, editconf can add a chain identifier to a
97 .pdb file, which can be useful for analysis with e.g. Rasmol.
98 To convert a truncated octrahedron file produced by a package which
100 uses a cubic box with the corners cut off (such as GROMOS), use:
101 gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
103 where veclen is the size of the cubic box times sqrt(3)/2.
105
107 Options to specify input files:
108 -f [<.gro/.g96/…>] (conf.gro)
110 Structure file: gro g96 pdb brk ent esp tpr
111 -n [<.ndx>] (index.ndx) (Optional)
113 Index file
114 -bf [<.dat>] (bfact.dat) (Optional)
116 Generic data file
117 Options to specify output files:
119 -o [<.gro/.g96/…>] (out.gro) (Optional)
121 Structure file: gro g96 pdb brk ent esp
122 -mead [<.pqr>] (mead.pqr) (Optional)
124 Coordinate file for MEAD
125 Other options:
127 -[no]w (no)
129 View output .xvg, .xpm, .eps and .pdb files
130 -[no]ndef (no)
132 Choose output from default index groups
133 -bt <enum> (triclinic)
135 Box type for -box and -d: triclinic, cubic, dodecahedron, octa‐
136 hedron
137 -box <vector> (0 0 0)
139 Box vector lengths (a,b,c)
140 -angles <vector> (90 90 90)
142 Angles between the box vectors (bc,ac,ab)
143 -d <real> (0)
145 Distance between the solute and the box
146 -[no]c (no)
148 Center molecule in box (implied by -box and -d)
149 -center <vector> (0 0 0)
151 Shift the geometrical center to (x,y,z)
152 -aligncenter <vector> (0 0 0)
154 Center of rotation for alignment
155 -align <vector> (0 0 0)
157 Align to target vector
158 -translate <vector> (0 0 0)
160 Translation
161 -rotate <vector> (0 0 0)
163 Rotation around the X, Y and Z axes in degrees
164 -[no]princ (no)
166 Orient molecule(s) along their principal axes
167 -scale <vector> (1 1 1)
169 Scaling factor
170 -density <real> (1000)
172 Density (g/L) of the output box achieved by scaling
173 -[no]pbc (no)
175 Remove the periodicity (make molecule whole again)
176 -resnr <int> (-1)
178 Renumber residues starting from resnr
179 -[no]grasp (no)
181 Store the charge of the atom in the B-factor field and the
182 radius of the atom in the occupancy field
183 -rvdw <real> (0.12)
185 Default Van der Waals radius (in nm) if one can not be found in
186 the database or if no parameters are present in the topology
187 file
188 -[no]sig56 (no)
190 Use rmin/2 (minimum in the Van der Waals potential) rather than
191 sigma/2
192 -[no]vdwread (no)
194 Read the Van der Waals radii from the file vdwradii.dat rather
195 than computing the radii based on the force field
196 -[no]atom (no)
198 Force B-factor attachment per atom
199 -[no]legend (no)
201 Make B-factor legend
202 -label <string> (A)
204 Add chain label for all residues
205 -[no]conect (no)
207 Add CONECT records to a .pdb file when written. Can only be done
208 when a topology is present
209
211 · For complex molecules, the periodicity removal routine may break
212 down, in that case you can use gmx trjconv.
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215 gmx(1)
216 More information about GROMACS is available at <‐
218 http://www.gromacs.org/>.
219
221 2020, GROMACS development team
2222019.6 Feb 28, 2020 GMX-EDITCONF(1)