the error says "donar" not found- and this is exactly right. some of your
commands are spelled correctly "donor" and some are misspelled "donar"
(notice the a)
On Sat, Nov 14, 2009 at 10:56 AM, shamoon siddiqui <
shamoonsiddiqui.gmail.com> wrote:
> I am trying to do hydrogen bonding analysis of a protein dna complex using
> ptraj. I have modified script for dna donar and accepters atom, but when i
> run this script it gives error. So could anyone please let me know that
> this
> script can be modified for dna also or it is only for protein. I am sending
> modified script for my protein dna complex as an attachment, please see and
> suggest me what should i do. modified script and error both are pasted
> below.
>
> Thanks in
> advance
>
>
> --
> With best regards
>
> Dr. Shamoon Ahmad Siddiqui
> DBT Postdoctoral Fellow
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore-560012, India
>
>
>
>
> trajin 2HT0_wat_1-5.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
> donar mask :DC.P
> donar mask :DC.O1P
> donar mask :DC.O2P
> donar mask :DC.O5'
> donar mask :DC.O4'
> donar mask :DC.N1
> donar mask :DC.N4
> donar mask :DC.N3
> donar mask :DC.O2
> donar mask :DC.O3'
> donar mask :DG.P
> donar mask :DG.O1P
> donar mask :DG.O2P
> donar mask :DG.O5'
> donar mask :DG.O4'
> donar mask :DG.N9
> donar mask :DG.N7
> donar mask :DG.O6
> donar mask :DG.N1
> donar mask :DG.N2
> donar mask :DG.N3
> donar mask :DG.O3'
> donar mask :DT.P
> donar mask :DT.O1P
> donar mask :DT.O2P
> donar mask :DT.O5'
> donar mask :DT.O4'
> donar mask :DT.N1
> donar mask :DT.O4
> donar mask :DT.N3
> donar mask :DT.O2
> donar mask :DT.O3'
> donar mask :DA.P
> donar mask :DA.O1P
> donar mask :DA.O2P
> donar mask :DA.O5'
> donar mask :DA.O4'
> donar mask :DA.N9
> donar mask :DA.N7
> donar mask :DA.N6
> donar mask :DA.N1
> donar mask :DA.N3
> donar mask :DA.O3'
>
> #-- 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
> acceptor mask :DC.N4 :DC.H41
> acceptor mask :DC.N4 :DC.H42
> acceptor mask :DG.N1 :DG.H1
> acceptor mask :DG.N2 :DG.H21
> acceptor mask :DG.N2 :DG.H22
> acceptor mask :DT.N3 :DT.H3
> acceptor mask :DA.N6 :DA.H61
> acceptor mask :DA.N6 :DA.H62
>
>
> #-- 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 :2-11,13-16,20.N :2-20.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
>
>
>
>
>
>
>
>
> Checking coordinates: 2HT0_wat_1-5.binpos
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.o1p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.o2p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.o5'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.o4'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.n1" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.n4" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.n3" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.o2" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dc.o3'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.o1p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.o2p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.o5'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.o4'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.n9" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.n7" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.o6" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.n1" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.n2" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.n3" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dg.o3'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o1p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o2p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o5'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o4'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.n1" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o4" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.n3" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o2" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":dt.o3'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.o1p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.o2p" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.o5'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.o4'" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.n9" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.n7" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.n6" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.n1" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.n3" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "donar" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string "mask" not found in tokenlist
>
>
> WARNING in dispatchToken: Token string ":da.o3'" not found in tokenlist
>
> Segmentation fault
>
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Received on Sat Nov 14 2009 - 08:30:03 PST
