i want to calculate inter-hydrogen bonding between antigen and antibody using pymol. how i can calculate it and how i can get the hydrogen bonding log file?is there any way to get pymol log file about inter-hydrogen bonding?
Have you tried this:
http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/hydrogenbond.php
or
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
yeah i tried 1st one but it really difficult for me to visualize and check the hydrogen bonding between the interface residues . is there any possible way to get log file of that hydrogen bonding.
This series of commands will display the H-bonds, of course you can change the cut-off to a more stringent value, and need to adjust the selection to the chain labels of antibody and antigen
h_add
select water, resn HOH
select antibody, chain A and not water
select antigen, chain B and not water
select don, (elem n+o and (neighbor hydro)) and not water
select acc, (elem o or (elem n and not (neighbor hydro))) and not water
dist HBA, (antigen and acc), (antibody and don), 3.2
dist HBD, (antigen and don), (antibody and acc), 3.2
It will generate some false-positives, because it does not look for correct angles
This will list out the atoms involved in these hydrogen bonds:
select sele, (((acc and antibody) within 3.2 of (don and antigen)) or ((acc and antigen) within 3.2 of (don and antibody)))
list=[]
iterate (sele), list.append(( chain, resi, resn, name))
print list
select sele, ((don and antibody) within 3.2 of (acc and antigen)) or ((don and antigen) within 3.2 of (acc and antibody))
list=[]
iterate (sele), list.append(( chain, resi, resn, name))
print list
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