Dear Carlos Simmerling
Thanks a lot for your kind help. After doing correction of spelling when i
again run this calculation this error removes, but the last error of
segmentation fault appears, i am again sending you modified script after
spelling correction. The error is
Checking coordinates: 2HT0_wat_1-5.binpos
Segmentation fault
I am keenly waiting for your kind reply
Thanks in advance
On Sat, Nov 14, 2009 at 4:00 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> >
> >
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>
--
With best regards
Dr. Shamoon Ahmad Siddiqui
DBT Postdoctoral Fellow
Molecular Biophysics Unit
Indian Institute of Science
Bangalore-560012, India
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Received on Sat Nov 14 2009 - 08:30:04 PST
