[AMBER] ptraj: Hbonds

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 20 Dec 2011 18:38:10 +0100

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.



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Received on Tue Dec 20 2011 - 10:00:03 PST
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