Hello all,
When I took Hbond calculation with Amber I suffered some problems.
The moleculars are a monomer and a dimer, I think many hbonds of them
should be similar more or less. But the results are very different.
the hbond.ptraj of monomer is this:
trajin md.binpos
#-- 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 :3-10,12-23,25-42,44-85,87-101,103-112,114-124,126-127.N :2-127.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 print .05 series hbt
And the hbond.ptraj of dimer is this
trajin md.binpos
#-- 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 :AS4.OD1
donor mask :AS4.OD2
donor mask :GL4.OE1
donor mask :GL4.OE2
donor mask :SER.OG
donor mask :THR.OG1
donor mask :HIP.ND1
donor mask :HIP.ND1
donor mask :HIP.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 :HIP.NE2 :HIP.HE2
acceptor mask :HIP.NE2 :HIP.HE2
acceptor mask :HIP.ND1 :HIP.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 :3-10,12-23,25-42,44-54,56-85,87-101,103-112,114-124,126-127,128,130-137,139-150,152-169,171-181,183-212,214-228,230-239,241-251,253-254.N
:2-254.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 print .05 series hbt
My question is that what should be modified of the script when taking
hbond analysis of dimer?
Or just treat the dimer like a usual molecular?
Thanks
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 25 2011 - 20:00:03 PDT
