Hi Amber users,
Further to my posting fro yesterday, I have a hond analysis scipt as
follows:
trajin /DATA/DIETHYLSTILBOESTROL_DYNAMICS/diethyl2-10.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 :BEN 1.O7 :1.H5
donor mask :BEN 1.O20 :1.H20
acceptor mask :BEN 1.O7 :1.H5
acceptor mask :BEN 1.O20 :1.H20
#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 out
/DATA/DIETHYLSTILBOESTROL_TRAJECTORY_ANALYSIS/diethyl_hbond_analysis.dat
go
I have 2 problems:
I am still not sure that I am identifying the donor and acceptor OH on
the steroid correctly
The programm stalls while reading the aa donor and acceptor sites. It
continues to run, but no more output is written, and I get a getargument
error. I have changed format from mdrcd to binpos to aid memory, but I
have already gotten outputs, so I dont think it is a memory issue...
any ideas pls??
thanks
cxx
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Received on Wed Jul 05 2006 - 06:07:17 PDT
