1editconf(1) GROMACS suite, VERSION 4.5 editconf(1)
2
6 editconf - edits the box and writes subgroups
7 VERSION 4.5
9
11 editconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf
12 bfact.dat -[no]h -[no]version -nice int -[no]w -[no]ndef -bt enum -box
13 vector -angles vector -d real -[no]c -center vector -aligncenter vector
14 -align vector -translate vector -rotate vector -[no]princ -scale vector
15 -density real -[no]pbc -[no]grasp -rvdw real -sig56 real -[no]vdwread
16 -[no]atom -[no]legend -label string -[no]conect
17
19 editconf converts generic structure format to .gro, .g96 or .pdb.
20 The box can be modified with options -box, -d and -angles. Both
23 -box and -d will center the system in the box, unless -noc is used.
24 Option -bt determines the box type: triclinic is a triclinic box,
27 cubic is a rectangular box with all sides equal dodecahedron repre‐
28 sents a rhombic dodecahedron and octahedron is a truncated octahedron.
29 The last two are special cases of a triclinic box. The length of the
30 three box vectors of the truncated octahedron is the shortest distance
31 between two opposite hexagons. The volume of a dodecahedron is 0.71
32 and that of a truncated octahedron is 0.77 of that of a cubic box with
33 the same periodic image distance.
34 Option -box requires only one value for a cubic box, dodecahedron and
37 a truncated octahedron.
38 With -d and a triclinic box the size of the system in the x, y and z
41 directions is used. With -d and cubic, dodecahedron or octahedron
42 boxes, the dimensions are set to the diameter of the system (largest
43 distance between atoms) plus twice the specified distance.
44 Option -angles is only meaningful with option -box and a triclinic
47 box and can not be used with option -d.
48 When -n or -ndef is set, a group can be selected for calculating the
51 size and the geometric center, otherwise the whole system is used.
52 -rotate rotates the coordinates and velocities.
55 -princ aligns the principal axes of the system along the coordinate
58 axes, this may allow you to decrease the box volume, but beware that
59 molecules can rotate significantly in a nanosecond.
60 Scaling is applied before any of the other operations are performed.
63 Boxes and coordinates can be scaled to give a certain density (option
64 -density). Note that this may be inaccurate in case a gro file is given
65 as input. A special feature of the scaling option, when the factor -1
66 is given in one dimension, one obtains a mirror image, mirrored in one
67 of the plains, when one uses -1 in three dimensions a point-mirror
68 image is obtained.
69 Groups are selected after all operations have been applied.
72 Periodicity can be removed in a crude manner. It is important that the
75 box sizes at the bottom of your input file are correct when the period‐
76 icity is to be removed.
77 When writing .pdb files, B-factors can be added with the -bf option.
80 B-factors are read from a file with with following format: first line
81 states number of entries in the file, next lines state an index fol‐
82 lowed by a B-factor. The B-factors will be attached per residue unless
83 an index is larger than the number of residues or unless the -atom
84 option is set. Obviously, any type of numeric data can be added instead
85 of B-factors. -legend will produce a row of CA atoms with B-factors
86 ranging from the minimum to the maximum value found, effectively making
87 a legend for viewing.
88 With the option -mead a special pdb (pqr) file for the MEAD electro‐
91 statics program (Poisson-Boltzmann solver) can be made. A further pre‐
92 requisite is that the input file is a run input file. The B-factor
93 field is then filled with the Van der Waals radius of the atoms while
94 the occupancy field will hold the charge.
95 The option -grasp is similar, but it puts the charges in the B-factor
98 and the radius in the occupancy.
99 Option -align allows alignment of the principal axis of a specified
102 group against the given vector, with an optional center of rotation
103 specified by -aligncenter.
104 Finally with option -label editconf can add a chain identifier to a
107 pdb file, which can be useful for analysis with e.g. rasmol.
108 To convert a truncated octrahedron file produced by a package which
111 uses a cubic box with the corners cut off (such as Gromos) use:
112 editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
114 where veclen is the size of the cubic box times sqrt(3)/2.
116
118 -f conf.gro Input
119 Structure file: gro g96 pdb tpr etc.
120 -n index.ndx Input, Opt.
122 Index file
123 -o out.gro Output, Opt.
125 Structure file: gro g96 pdb etc.
126 -mead mead.pqr Output, Opt.
128 Coordinate file for MEAD
129 -bf bfact.dat Input, Opt.
131 Generic data file
132
135 -[no]hno
136 Print help info and quit
137 -[no]versionno
139 Print version info and quit
140 -nice int 0
142 Set the nicelevel
143 -[no]wno
145 View output xvg, xpm, eps and pdb files
146 -[no]ndefno
148 Choose output from default index groups
149 -bt enum triclinic
151 Box type for -box and -d: triclinic, cubic, dodecahedron or octa‐
152 hedron
153 -box vector 0 0 0
155 Box vector lengths (a,b,c)
156 -angles vector 90 90 90
158 Angles between the box vectors (bc,ac,ab)
159 -d real 0
161 Distance between the solute and the box
162 -[no]cno
164 Center molecule in box (implied by -box and -d)
165 -center vector 0 0 0
167 Coordinates of geometrical center
168 -aligncenter vector 0 0 0
170 Center of rotation for alignment
171 -align vector 0 0 0
173 Align to target vector
174 -translate vector 0 0 0
176 Translation
177 -rotate vector 0 0 0
179 Rotation around the X, Y and Z axes in degrees
180 -[no]princno
182 Orient molecule(s) along their principal axes
183 -scale vector 1 1 1
185 Scaling factor
186 -density real 1000
188 Density (g/l) of the output box achieved by scaling
189 -[no]pbcno
191 Remove the periodicity (make molecule whole again)
192 -[no]graspno
194 Store the charge of the atom in the B-factor field and the radius of
195 the atom in the occupancy field
196 -rvdw real 0.12
198 Default Van der Waals radius (in nm) if one can not be found in the
199 database or if no parameters are present in the topology file
200 -sig56 real 0
202 Use rmin/2 (minimum in the Van der Waals potential) rather than
203 sigma/2
204 -[no]vdwreadno
206 Read the Van der Waals radii from the file vdwradii.dat rather than
207 computing the radii based on the force field
208 -[no]atomno
210 Force B-factor attachment per atom
211 -[no]legendno
213 Make B-factor legend
214 -label string A
216 Add chain label for all residues
217 -[no]conectno
219 Add CONECT records to a pdb file when written. Can only be done when a
220 topology is present
221
224 - For complex molecules, the periodicity removal routine may break
225 down,
226 - in that case you can use trjconv.
228
231 gromacs(7)
232 More information about GROMACS is available at <http://www.gro‐
234 macs.org/>.
235 Thu 26 Aug 2010 editconf(1)