This utility computes spatial distribution functions and creates a file which can be visualized using gOpenMol package (http://.www.csc.fi/gopenmol/).
f77 -O3 -o sdf sdf.f tranal_base.f
The input into
sdf utility consists of a NAMELIST section
SDFIN and subsequent lines defining sites which will be displayed
for visualization of the molecule around which SDF is calculated
The NAMELIST section
$SDFIN parameter=value(s), ... $END
contains the following parameters
FILORI = <filename>
The name of the output file with SDF written as ``formatted'' plt-file for gOpenMol package. Before visualization, it must be converted to the binary using ``pltfile'' utility of gOpenMol (available also from gOpenMol menu).
FILCRD = <filename>The name of file into which average coordinates of molecule, defining the local basis, are written. These coordinates are computed using the basis of the molecule itself, and they in fact used for visualization of the local basis. This file is written in ``XMOL'' format. The last column shows the variance (average deviations) of atoms around their average positions in the local coordinate system, which may serve also for evaluation of molecular flexibility.
NOI = <int.value>Defines the number of equivalent local coordinate systems on the molecule (for example, for DNA SDFs can be defined around each of phosphate group used as a local basis)
IO1 = <n1_1>,<n1_2>,...,<n1_NOI> IO2 = <n2_1>,<n2_2>,...,<n2_NOI> IO3 = <n3_1>,<n3_2>,...,<n3_NOI>
NOI values in each of these three lines. They define
local basises. Each basis is defined by three sites (for example,
<n1_1>,<n2_1>,<n3_1>. The center of local coordinate system is set
at the first site, the X-axis goes as a mediana of 2-1-3 angle, and the
Z-axis is perpendicular to the plane defined by these three sites.
NSOR = <int.value>
Number of sites for calculation of SDF.
ISOR = <n1>,<n2> ...
NSOR integer values. They define SDF of which sites to compute,
and then take an average over them.
RXMAX = <value> RYMAX = <value> RZMAX = <value>These parameters define the box inside which SDF is calculated (for example, from
NOMX = <value> NOMY = <value> NOMZ = <value>resolution (number of bins) in each direction
After the NAMELIST section, there is a section in the input file
which describes which atoms are displayed in the center of SDF as
a structure defining the local basis.
The first line of this section may be either an integer number or
the word ``
If an integer number is specified, it defines the number of atoms
displayed in the central structure. Then this number of lines follows,
each line per atom, each consisting of
NOI + 1 values.
The first position in each line is one of numbers 1,2,3.
Positions from 2 to
NOI + 1 define sites which are to be displayed,
for each of
NOI equivalent local coordinate system.
The number in the first position of each line means the following:
1 - coordinates of this atom are averaged independently of the next atom
2 - average coordinates of this atom are calculated taking into account the next atom also (for example, if these are two hydrogens of water)
3 - average coordinates of this atom are calculated taking into account the next two atoms (for instance, treating hydrogens in CH3 group)
Example of these lines for water:
1 1 2 2 1 3
and for methanol (see the order of atoms in CH3OH.mmol file)
1 1 1 2 1 3 3 4 2 5 1 6
ALL is specified in the first (and the only) line of
this section, then all the atoms of the molecule defining the local basis
are displayed, without any special treatment of averaging coordinates of
Note about Gopenmol From 2011, there is no longer support for gOpenMol package, though the source and binary executable are still available from the developers.