I'm trying to analyse HBond formation using the following script
ptraj my_prmtop hbond.in > hbond.out
where hbond.in is:
#-- Donors from standard amino acids and WAT
trajin equil_2ns.mdcrd
donor mask :GLN.OE1
donor mask :GLN.NE2
........
donor mask :HID.NE2
donor WAT O
#-- Acceptor:IND
acceptor mask :IND.N :IND.H
hbond print .05 series hbt
where IND stand for indole.
No Hbonds appear in the output (see attached file) despite the fact that I see multiple in VMD and Chimera.
I can only assume that there's something wrong with masks but I fail to see what.
Any help will be most welcome.
Regards
George
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Received on Tue Dec 20 2011 - 10:00:03 PST
