*FILENAME: hbonds.inp *PURPOSE: compute static and time-dependent hydrogen bonds from trajectory *AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003 *MODIFIED: Mike McCallum UOP Oct. 2004 * !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! set rtf /usr/local/charmm/toppar/top_all22_prot_cmap !! set prm /usr/local/charmm/toppar/par_all22_prot_cmap !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! open unit 1 card read name - @rtf.inp read RTF card unit 1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! open unit 2 card read name - @prm.inp read PARA card unit 2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! !! Input files/etc if @?input eq 0 goto endoffile if @?begin eq 0 goto endoffile open unit 4 card read name @input.psf read PSF card unit 4 !! open unit 1 read card name @input.pdb read coor pdb unit 1 close unit 1 ! hydrogen bonding patterns in initial structure ! the "coor hbond" depends on DONOr/ACCEptor information in PSF to ! identify possible hbonding partners; see corman.doc for details ! we use strictly geometric criteria on the H...A distance, and optionally ! on the D-H...A angle to define the hydrogen bond ! first look at the backbone-backbone hydrogen bonds coor hbond verbose select type HN end select type O end ! now get the time-dependent hydrogen bonds; ! the output can be voluminous, especially ! with the verbose option open unit 51 read unform name @input.dcd traj query unit 51 !open unit 52 read unform name a10-a-stt2.dcd !! any other files opened in sequence: !!open unit 52 read unform name my_traj2.cor ! the SKIP 2500 (=5ps) means that for a hydrogen bond to be counted as broken ! in the calculation of average lifetime it has to be broken ! for > 5ps (otherwise we are unlikely to detect the break) ! Note that by default, HBOND does not specificy a threshold ! angle (cutha). This is too generous. I reccomend 160 deg (corresponding ! to a VMD angle of 20). The default distance (O -- H, not O---N) ! distance is 2.4 A (cuthb). ! ! Representative CHARMM output (in the log file): ! ! Analysis of hydrogen bonds using cutoff distance= 2.40 and angle= 160.00 ! Total time= 400.0ps. Resolution= 1.00ps ! Occupancy cutoff= 0.00 Lifetime cutoff= 0.0ps ! ! I-atom J-atom