AMBER Archive (2009)

Subject: Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Nov 14 2009 - 10:00:39 CST

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_at_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_at_OE1
> donor mask :GLN_at_NE2
> donor mask :ASN_at_OD1
> donor mask :ASN_at_ND2
> donor mask :TYR_at_OH
> donor mask :ASP_at_OD1
> donor mask :ASP_at_OD2
> donor mask :GLU_at_OE1
> donor mask :GLU_at_OE2
> donor mask :SER_at_OG
> donor mask :THR_at_OG1
> donor mask :HIS_at_ND1
> donor mask :HIE_at_ND1
> donor mask :HID_at_NE2
> donar mask :DC_at_P
> donar mask :DC_at_O1P
> donar mask :DC_at_O2P
> donar mask :DC_at_O5'
> donar mask :DC_at_O4'
> donar mask :DC_at_N1
> donar mask :DC_at_N4
> donar mask :DC_at_N3
> donar mask :DC_at_O2
> donar mask :DC_at_O3'
> donar mask :DG_at_P
> donar mask :DG_at_O1P
> donar mask :DG_at_O2P
> donar mask :DG_at_O5'
> donar mask :DG_at_O4'
> donar mask :DG_at_N9
> donar mask :DG_at_N7
> donar mask :DG_at_O6
> donar mask :DG_at_N1
> donar mask :DG_at_N2
> donar mask :DG_at_N3
> donar mask :DG_at_O3'
> donar mask :DT_at_P
> donar mask :DT_at_O1P
> donar mask :DT_at_O2P
> donar mask :DT_at_O5'
> donar mask :DT_at_O4'
> donar mask :DT_at_N1
> donar mask :DT_at_O4
> donar mask :DT_at_N3
> donar mask :DT_at_O2
> donar mask :DT_at_O3'
> donar mask :DA_at_P
> donar mask :DA_at_O1P
> donar mask :DA_at_O2P
> donar mask :DA_at_O5'
> donar mask :DA_at_O4'
> donar mask :DA_at_N9
> donar mask :DA_at_N7
> donar mask :DA_at_N6
> donar mask :DA_at_N1
> donar mask :DA_at_N3
> donar mask :DA_at_O3'
>
> #-- Acceptors from standard amino acids
> acceptor mask :ASN_at_ND2 :ASN_at_HD21
> acceptor mask :ASN_at_ND2 :ASN_at_HD22
> acceptor mask :TYR_at_OH :TYR_at_HH
> acceptor mask :GLN_at_NE2 :GLN_at_HE21
> acceptor mask :GLN_at_NE2 :GLN_at_HE22
> acceptor mask :TRP_at_NE1 :TRP_at_HE1
> acceptor mask :LYS_at_NZ :LYS_at_HZ1
> acceptor mask :LYS_at_NZ :LYS_at_HZ2
> acceptor mask :LYS_at_NZ :LYS_at_HZ3
> acceptor mask :SER_at_OG :SER_at_HG
> acceptor mask :THR_at_OG1 :THR_at_HG1
> acceptor mask :ARG_at_NH2 :ARG_at_HH21
> acceptor mask :ARG_at_NH2 :ARG_at_HH22
> acceptor mask :ARG_at_NH1 :ARG_at_HH11
> acceptor mask :ARG_at_NH1 :ARG_at_HH12
> acceptor mask :ARG_at_NE :ARG_at_HE
> acceptor mask :HIS_at_NE2 :HIS_at_HE2
> acceptor mask :HIE_at_NE2 :HIE_at_HE2
> acceptor mask :HID_at_ND1 :HID_at_HD1
> acceptor mask :HIP_at_ND1,NE2 :HIP_at_HE2,HD1
> acceptor mask :DC_at_N4 :DC_at_H41
> acceptor mask :DC_at_N4 :DC_at_H42
> acceptor mask :DG_at_N1 :DG_at_H1
> acceptor mask :DG_at_N2 :DG_at_H21
> acceptor mask :DG_at_N2 :DG_at_H22
> acceptor mask :DT_at_N3 :DT_at_H3
> acceptor mask :DA_at_N6 :DA_at_H61
> acceptor mask :DA_at_N6 :DA_at_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_at_N :2-20_at_H
> #Terminal residues have different atom names
> donor mask @OXT
> acceptor mask :1_at_N :1_at_H1
> acceptor mask :1_at_N :1_at_H2
> acceptor mask :1_at_N :1_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_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_at_o3'" not found in tokenlist
>
> Segmentation fault
>
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