In order to illustrate the output of OBGMX, let us consider the
creation of the topology for a sample
I chose caffeine, mostly because a lot of which has fuelled the creation of this software.
The coordinate file for caffeine can be downloaded from PubChem. Since we are using Open Babel, the sdf format used by PubChem is perfectly valid as input and can be fed directly to OBGMX.
After submitting your molecule (or periodic system), two files will be returned by
OBGMX. Actually, the user is presented with a web page where
two textareas contain all the relevant information.
The contents can be easily selected and copied into a text file.
For a detailed description of the format of these files, please check the GROMACS site
The first file is obgmx.top. Roughly
speaking, it contains all the parameters needed to compute the
non-bonded interactions, as well as a list of the kind and number of
molecules that are to be simulated.
The names of the atom types should reflect the names proposed in the UFF parametrization.
OBGMX will return just one molecule, the one used as input, and it will be named UFF.
OBGMX does not offer any tool to create starting configurations of (mixtures of) molecules. Please refer to the GROMACS documentation for this purpose.
The second file produced by OBGMX
is obgmx.itp, which contains a description
of the bonded interactions of the given molecule.
For the user's convenience, OBGMX identifies all the unique contributions to the various bonded interactions (stretching, bending, torsions and impropers) and outputs them as comments in the first lines of the relevant section.
The .itp file for caffeine is