| | 1 | = Fragmenting Molecules = |
| | 2 | |
| | 3 | In the following we use molecuilder to generate all possible fragments of a given molecule: |
| | 4 | {{{ |
| | 5 | ./molecuilder -i <input> -I --fragment-molecule ./ --distance 2. --order 4 |
| | 6 | }}} |
| | 7 | which takes the file ''<input>'', creates the bond graph (''--I''), and fragments the molecule up to order 4 (''--order''). |
| | 8 | |
| | 9 | This will create files ''!BondFragment###.conf'' (and with ''.in'' suffix, too) in the current (''./'') directory where ''###'' starts at 0 and counts through all created fragments. |
| | 10 | |
| | 11 | These can subsequently be used with PCP or MPQC to calculate the fragment energy. |
