Hi People,
I am using ptraj hbond to calculate the % of hydrogen bond occurrence in the trajectory.
hough I could see the many Hbonds in VMD, but the results from hbond ptraj could show only two hbond.
The Hbond analysis shows only few.
My input goes like this
trajin ST5M-20ns.crd 1 20000
strip :WAT
strip :Cl-
strip :Na+
#-- Donors from standard amino acids
donor mask :GLN.OE1
donor mask :GLN.NE2
donor mask :ASN.OD1
donor mask :ASN.ND2
donor mask :TYR.OH
donor mask :ASP.OD1
donor mask :ASP.OD2
donor mask :GLU.OE1
donor mask :GLU.OE2
donor mask :SER.OG
donor mask :THR.OG1
donor mask :HIS.ND1
donor mask :HIE.ND1
donor mask :HID.NE2
#-- Acceptors from standard amino acids
acceptor mask :ASN.ND2 :ASN.HD21
acceptor mask :ASN.ND2 :ASN.HD22
acceptor mask :TYR.OH :TYR.HH
acceptor mask :GLN.NE2 :GLN.HE21
acceptor mask :GLN.NE2 :GLN.HE22
acceptor mask :TRP.NE1 :TRP.HE1
acceptor mask :LYS.NZ :LYS.HZ1
acceptor mask :LYS.NZ :LYS.HZ2
acceptor mask :LYS.NZ :LYS.HZ3
acceptor mask :SER.OG :SER.HG
acceptor mask :THR.OG1 :THR.HG1
acceptor mask :ARG.NH2 :ARG.HH21
acceptor mask :ARG.NH2 :ARG.HH22
acceptor mask :ARG.NH1 :ARG.HH11
acceptor mask :ARG.NH1 :ARG.HH12
acceptor mask :ARG.NE :ARG.HE
acceptor mask :HIS.NE2 :HIS.HE2
acceptor mask :HIE.NE2 :HIE.HE2
acceptor mask :HID.ND1 :HID.HD1
acceptor mask :HIP.ND1,NE2 :HIP.HE2,HD1
#-- Backbone donors and acceptors for this particular molecule
# N-H for prolines do not exist so are not in the mask
#
donor mask .O
acceptor mask :1-18.N :1-18.H
#Terminal residues have different atom names
donor mask .OXT
acceptor mask :1.N :1.H1
acceptor mask :1.N :1.H2
acceptor mask :1.N :1.H3
#-- series hbt is just a placeholder to ensure we get the full analysis. If you don't
#have the word series you don't get a full analysis.
#hbond distance 3.5 angle print .05 series hbt out ST5M_test_dis35.dat
hbond print .05 series hbt
Thank you for your help,
Mannan
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Received on Fri Sep 03 2010 - 02:30:03 PDT
