1 .TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 editconf - edits the box and writes subgroups
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-n" " index.ndx "
11 .BI "\-mead" " mead.pqr "
12 .BI "\-bf" " bfact.dat "
14 .BI "\-[no]version" ""
19 .BI "\-box" " vector "
20 .BI "\-angles" " vector "
23 .BI "\-center" " vector "
24 .BI "\-aligncenter" " vector "
25 .BI "\-align" " vector "
26 .BI "\-translate" " vector "
27 .BI "\-rotate" " vector "
29 .BI "\-scale" " vector "
30 .BI "\-density" " real "
35 .BI "\-sig56" " real "
36 .BI "\-[no]vdwread" ""
39 .BI "\-label" " string "
42 \&\fB editconf\fR converts generic structure format to \fB .gro\fR, \fB .g96\fR
47 \&The box can be modified with options \fB \-box\fR, \fB \-d\fR and
48 \&\fB \-angles\fR. Both \fB \-box\fR and \fB \-d\fR
49 \&will center the system in the box, unless \fB \-noc\fR is used.
53 \&Option \fB \-bt\fR determines the box type: \fB triclinic\fR is a
54 \&triclinic box, \fB cubic\fR is a rectangular box with all sides equal
55 \&\fB dodecahedron\fR represents a rhombic dodecahedron and
56 \&\fB octahedron\fR is a truncated octahedron.
57 \&The last two are special cases of a triclinic box.
58 \&The length of the three box vectors of the truncated octahedron is the
59 \&shortest distance between two opposite hexagons.
60 \&Relative to a cubic box with some periodic image distance, the volume of a
61 \&dodecahedron with this same periodic distance is 0.71 times that of the cube,
62 \&and that of a truncated octahedron is 0.77 times.
66 \&Option \fB \-box\fR requires only
67 \&one value for a cubic, rhombic dodecahedral, or truncated octahedral box.
71 \&With \fB \-d\fR and a \fB triclinic\fR box the size of the system in the \fI x\fR\-, \fI y\fR\-,
72 \&and \fI z\fR\-directions is used. With \fB \-d\fR and \fB cubic\fR,
73 \&\fB dodecahedron\fR or \fB octahedron\fR boxes, the dimensions are set
74 \&to the diameter of the system (largest distance between atoms) plus twice
75 \&the specified distance.
79 \&Option \fB \-angles\fR is only meaningful with option \fB \-box\fR and
80 \&a triclinic box and cannot be used with option \fB \-d\fR.
84 \&When \fB \-n\fR or \fB \-ndef\fR is set, a group
85 \&can be selected for calculating the size and the geometric center,
86 \&otherwise the whole system is used.
90 \&\fB \-rotate\fR rotates the coordinates and velocities.
94 \&\fB \-princ\fR aligns the principal axes of the system along the
95 \&coordinate axes, with the longest axis aligned with the \fI x\fR\-axis.
96 \&This may allow you to decrease the box volume,
97 \&but beware that molecules can rotate significantly in a nanosecond.
101 \&Scaling is applied before any of the other operations are
102 \&performed. Boxes and coordinates can be scaled to give a certain density (option
103 \&\fB \-density\fR). Note that this may be inaccurate in case a \fB .gro\fR
104 \&file is given as input. A special feature of the scaling option is that when the
105 \&factor \-1 is given in one dimension, one obtains a mirror image,
106 \&mirrored in one of the planes. When one uses \-1 in three dimensions,
107 \&a point\-mirror image is obtained.
110 \&Groups are selected after all operations have been applied.
113 \&Periodicity can be removed in a crude manner.
114 \&It is important that the box vectors at the bottom of your input file
115 \&are correct when the periodicity is to be removed.
119 \&When writing \fB .pdb\fR files, B\-factors can be
120 \&added with the \fB \-bf\fR option. B\-factors are read
121 \&from a file with with following format: first line states number of
122 \&entries in the file, next lines state an index
123 \&followed by a B\-factor. The B\-factors will be attached per residue
124 \&unless an index is larger than the number of residues or unless the
125 \&\fB \-atom\fR option is set. Obviously, any type of numeric data can
126 \&be added instead of B\-factors. \fB \-legend\fR will produce
127 \&a row of CA atoms with B\-factors ranging from the minimum to the
128 \&maximum value found, effectively making a legend for viewing.
132 \&With the option \fB \-mead\fR a special \fB .pdb\fR (\fB .pqr\fR)
133 \&file for the MEAD electrostatics
134 \&program (Poisson\-Boltzmann solver) can be made. A further prerequisite
135 \&is that the input file is a run input file.
136 \&The B\-factor field is then filled with the Van der Waals radius
137 \&of the atoms while the occupancy field will hold the charge.
141 \&The option \fB \-grasp\fR is similar, but it puts the charges in the B\-factor
142 \&and the radius in the occupancy.
146 \&Option \fB \-align\fR allows alignment
147 \&of the principal axis of a specified group against the given vector,
148 \&with an optional center of rotation specified by \fB \-aligncenter\fR.
152 \&Finally, with option \fB \-label\fR, \fB editconf\fR can add a chain identifier
153 \&to a \fB .pdb\fR file, which can be useful for analysis with e.g. Rasmol.
157 \&To convert a truncated octrahedron file produced by a package which uses
158 \&a cubic box with the corners cut off (such as GROMOS), use:
160 \&\fB editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out\fR
162 \&where \fB veclen\fR is the size of the cubic box times sqrt(3)/2.
164 .BI "\-f" " conf.gro"
166 Structure file: gro g96 pdb tpr etc.
168 .BI "\-n" " index.ndx"
174 Structure file: gro g96 pdb etc.
176 .BI "\-mead" " mead.pqr"
178 Coordinate file for MEAD
180 .BI "\-bf" " bfact.dat"
186 Print help info and quit
188 .BI "\-[no]version" "no "
189 Print version info and quit
191 .BI "\-nice" " int" " 0"
195 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
197 .BI "\-[no]ndef" "no "
198 Choose output from default index groups
200 .BI "\-bt" " enum" " triclinic"
201 Box type for \-box and \-d: \fB triclinic\fR, \fB cubic\fR, \fB dodecahedron\fR or \fB octahedron\fR
203 .BI "\-box" " vector" " 0 0 0"
204 Box vector lengths (a,b,c)
206 .BI "\-angles" " vector" " 90 90 90"
207 Angles between the box vectors (bc,ac,ab)
209 .BI "\-d" " real" " 0 "
210 Distance between the solute and the box
213 Center molecule in box (implied by \-box and \-d)
215 .BI "\-center" " vector" " 0 0 0"
216 Coordinates of geometrical center
218 .BI "\-aligncenter" " vector" " 0 0 0"
219 Center of rotation for alignment
221 .BI "\-align" " vector" " 0 0 0"
222 Align to target vector
224 .BI "\-translate" " vector" " 0 0 0"
227 .BI "\-rotate" " vector" " 0 0 0"
228 Rotation around the X, Y and Z axes in degrees
230 .BI "\-[no]princ" "no "
231 Orient molecule(s) along their principal axes
233 .BI "\-scale" " vector" " 1 1 1"
236 .BI "\-density" " real" " 1000 "
237 Density (g/L) of the output box achieved by scaling
239 .BI "\-[no]pbc" "no "
240 Remove the periodicity (make molecule whole again)
242 .BI "\-resnr" " int" " \-1"
243 Renumber residues starting from resnr
245 .BI "\-[no]grasp" "no "
246 Store the charge of the atom in the B\-factor field and the radius of the atom in the occupancy field
248 .BI "\-rvdw" " real" " 0.12 "
249 Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file
251 .BI "\-sig56" " real" " 0 "
252 Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
254 .BI "\-[no]vdwread" "no "
255 Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
257 .BI "\-[no]atom" "no "
258 Force B\-factor attachment per atom
260 .BI "\-[no]legend" "no "
261 Make B\-factor legend
263 .BI "\-label" " string" " A"
264 Add chain label for all residues
266 .BI "\-[no]conect" "no "
267 Add CONECT records to a \fB .pdb\fR file when written. Can only be done when a topology is present
270 \- For complex molecules, the periodicity removal routine may break down, in that case you can use \fB trjconv\fR.
275 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.