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MMTSB/CTBP Summer Workshop N H O C N © Lennart Nilsson , 2006.
Finding hydrogen bonds in a single MMTSB/CTBP Summer Workshop structure with <strong>CHARMM</strong> The COOR HBONd command (corman.doc) finds and lists all hydrogen bonds between two atom-selections based on r(H-A), and optionally ∧(D-H-A). The command uses acceptor/donor lists in the PSF to identify possible hydrogen bonding atoms. If DONO/ACCE statements are missing for some residue(s) in your RTF you have to add these and regenerate the PSF before using COOR HBONd (this may be the case for TIP3 residues). © Lennart Nilsson , 2006.
Page 1 and 2: MMTSB/CTBP Summer Workshop CHARMM A
Page 3 and 4: MMTSB/CTBP Summer Workshop Basic an
Page 5 and 6: MMTSB/CTBP Summer Workshop Single s
Page 7 and 8: MMTSB/CTBP Summer Workshop Energy e
Page 9 and 10: MMTSB/CTBP Summer Workshop Hydrogen
Page 11: MMTSB/CTBP Summer Workshop Hydrogen
Page 15 and 16: MMTSB/CTBP Summer Workshop Protein
Page 17 and 18: Snapshots can be anlyzed in a loop
Page 19 and 20: Hydrogen bonds from a trajectory co
Page 21 and 22: MMTSB/CTBP Summer Workshop Solvent
Page 23 and 24: MMTSB/CTBP Summer Workshop Geometry
Page 25 and 26: MMTSB/CTBP Summer Workshop Water g
Page 27 and 28: Hydration number / 3D histogram MMT
Page 29 and 30: MMTSB/CTBP Summer Workshop MSD calc
Page 31 and 32: MMTSB/CTBP Summer Workshop Clusteri
Page 33 and 34: Clustering with CHARMM, example cor
Page 35 and 36: MMTSB/CTBP Summer Workshop q 1.5 1.
Page 37 and 38: Example time-dependent fluorescence
Page 39 and 40: MMTSB/CTBP Summer Workshop Example
Page 41 and 42: MMTSB/CTBP Summer Workshop www.char

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