Q2M(1OSC) OSC utilities Q2M(1OSC) NAME q2m - convert cartesian coordinate table to Sybyl MOL file SYNOPSIS q2m [ -i inpfile ] [ -o outfile ] [ -s string ] [ -f optfile ] [ -n molname ] [ -d length ] [ -m unit ] [ -l link-list ] [ -u unlink-list ] [ -a maxatoms ] [ -b maxbonds ] [ inpfile [ outfile ] ] DESCRIPTION The program q2m converts a table of cartesian coordinates of atoms to a SYBYL MOL file format (SYBYL is a trademark of Tripos Associates). It creates appropriate atom types and bond types based on interatomic distances. The table of cartesian coordinates has to contain one column which iden- tifies element either by its chemical symbol, or atomic mass, or atomic number. The MOL file so created can be read into SYBYL for display or further manipulation. OPTIONs Option arguments contain characters which are frequently conflicting with the shell interpretation. For safety, it is advised that inclose them in single quotes. -i inpfile File inpfile contains cartesian coordinates. If inpfile is not specified, standard input (stdin) is assumed. inpfile can be also specified without -i option letter as the first argument after all options. -o outfile File outfile will contain resulting MOL file. If out- file is not specified standard output (stdout) is assumed. outfile can be also specified without -o option together with inpfile after all options as the second argument. -s string The order and type of columns in the table is given by string. Column is a series of nonblank characters fol- lowed by one or more spaces or TABs. The following colum types are recognized: M - atomic mass, A - atomic number, C - chemical symbol (may be followed by digits or other characters), S - column to discard, X - X coordinate, Y - Y coordinate, Z - Z coordinate. Only one M, A, or C column may be specified. The X, Y, or Z columns cannot be repeated. -f optfile The options will be read from optfile. The optfile con- tains options in the same format as if they appeared on the command line. OSC Last change: 27 Mar 1991 1 Q2M(1OSC) OSC utilities Q2M(1OSC) -n molname Using this option you can specify molecule name to be included in the MOL file or otherwise it will be set to "Unknown". -d length This is the length of longest possible bond [in Angstroms] in the molecule. All atoms closer to each other than length are considered bonded by a chemical bond. Exception is used for hydrogen atoms. Two hydro- gen atoms are considered bonded only if they are closer than 0.8 Angstrom. If length is not specified 1.7 Angstrom is assumed. -m unit The coordinates in the input file may be specified in B (bohrs, i.e. atomic units) N (nanometers) A (Angstroms). If this option is not specified, Angstroms are assumed. -l link-list Sometimes you want to include bonds which will not be found by a simple distance checking. You may specify a list of bonded atom pairs and a type of bond by which atoms are bonded. The link-list consist of entries of a type ibj separated by commas or spaces. i is the number of first atom, j is a number of second atom and b specifies a type of bond between them. The bond type b may one of the following: : (unspecified - when bond type is not known), - (single), = (double), # (triple), a (amide bond), r (aromatic), . (dummy - not a true bond, but marker rather), u (unusual - nobody yet knows what it is). This option may be used not only to add new bonds but also to specify a correct bond type for bonds which are found from interactomic distance com- parisons. The link-list should be enclosed in single quotes for safety. -u unlink-list Sometimes you want to remove some bonds which were found by simple distance check. This option removes bonds between atom pairs specified by unlink-list. Atom numbers and their pairs can be separated by spaces or any other nondigit characters. -a maxatoms If your coordinate table may contain more than 100 atoms, you need to specify larger limit for number of atoms with this option. -b maxbonds If your molecule may contain more than 200 bonds, you OSC Last change: 27 Mar 1991 2 Q2M(1OSC) OSC utilities Q2M(1OSC) need to specify larger limit for number of bonds with this option. EXAMPLES q2m -s SXYZM -m B -d 1.6 -l 1-4,1=2 -n propanal test.inp requests that file test.inp is converted to MOL file and sent to standard ouput. The coordinates are given origi- nally in atomic units. The columns 2-4 contain cartesian coordinates, while 5-th column contains atomic masses. Atoms are considered bonded if they are closer than 1.6 Angstrom to each another. The single bond is specified between atoms 1 and 4, and double bond between atoms 1 and 2. FILES The program resides in /loclib/q2m directory. Examples of use are given in /loclib/q2m/test. The docs are in /loclib/q2m/doc. SEE ALSO To familiarize yourself with MOL file format read appropri- ate pages of SYBYL manual or use on-line help facility of SYBYL. DIAGNOSTICS Most error messages are self-explanatory. BUGS Program does not find some atoms types and you have to enter correct types by editing resulting MOL file. This program does not contain substructure searches necessary to match some of the SYBYL atom types, however, most basic atom types are assigned correctly. Report bugs to the author. AUTHOR Jan Labanowski, Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163, ph. 614-292-9279, FAX: 614-292- 7168, e-mail: jkl@ccl.net, JKL@OHSTPY.BITNET. OSC Last change: 27 Mar 1991 3