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Database Preparation
mol2db
Brian Shoichet, Elaine Meng
The interactive program mol2db converts SYBYL ASCII (MOL2) formatted
coordinate files to the database format used by DOCK (SEARCH mode). Only the
largest fragment in each molecule record is written out. Hydrogens and charges
should be present if they are required by the scoring option to be used. The
user is asked for the input and output file names. mol2db asks for atom
flagging information before the atom coloring (labeling) information. You
should enter none for the flagging, since atom flagging is only partially
implemented. For the coloring, you must enter the color name (whatever you
want, up to 30 characters) followed by one or more spaces and then the SYBYL
atom type. Optionally, you can follow this, on the same line, by an integer
and another SYBYL atom type. The second atom type refers to a nearby atom, and
the integer is the number of intervening bonds. If negative, it means that the
first atom must not be this many bonds away from the second atom. Enter
none or a blank line to terminate. The same color may be entered more than
once, but there can be a maximum of 100 colors, and a maximum of 200 coloring
statements. Following the atom coloring information one is asked whether one
wishes to adjust charges, as described in the next paragraph. Answer yes or
no.
Besides performing a reformatting function, mol2db equalizes charges on
oxygens that are equivalent by resonance (in carboxylate, phosphate, sulfate,
and nitro groups) and adds a net positive charge to amidinium and guanidinium
groups. Atoms belonging to functional groups of interest may be flagged. The
largest covalent structure per @<TRIPOS>MOLECULE record is identified and
written out.
Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (rev. 1 September 1995)