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Brief instruction to obtain H-bond by CHARMM script for a Single Lipid Bilayer
Authors: Xiaohong Zhuang and Dr. Jeffery B. Klauda
This instruction is to explain the procedure to calculate the number of H-bonding in single lipid bilayer including the PBC.
Script in DT1: /lustre/xzhuang/simulation/script_folders/lipids_analyses/hb_chm_1_lip
Example in DT1: /lustre/xzhuang/simulation/script_folders/lipids_analyses/hb_chm_1_lip_eg
Script in DT2: /lustre/xzhuang/scripts/lipids_analyses/hb_chm_1_lip
Example in DT2: /lustre/xzhuang/scripts/lipids_analyses/hb_chm_1_lip_eg
Download Scripts:
Steps
1. Copy the script folder provided to your path.
1.1 Go to your path that you would like to work on H-bond analysis
1.2 For example, use the following command to copy the script folder to your path
cp -r /lustre/xzhuang/simulation/script_folders/lipids_analyses/hb_chm_1_lip ./
2. Updates to the 1_calc_hb_run.csh file
2.1 Update the path of your input file set sdir = “/lustre/xzhuang/simulation/dmpi/charmm-gui”
2.2 Update equilibrated dcd file range @ f = 36 # first dcd file to read @ l = 50 # last dcd file to read
2.3 Update lipid information including lipid type, lipid name, and headgroup name 2.3.1. Lipid type [type] for Glycerol lipids:G ; Sphingo lipids:S ; 2.3.2. Update lipid residue name [rn] 2.3.3. Update headgroups [h] for Glycerol:PA/PC/PE/PG/PI/PS; Sphingo: SM/CER ; DON'T includes the sterol,cholestrol lipids here as it has no H acceptor. DON'T includes the PC glycerol lipids here as it has no H donor. # Update the lipid that have both H donor and acceptor for intra-lipid H-bonding set type = G set rn = DMPI set h = PI