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AMBER Archive (2009)
Subject: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj
From: shamoon siddiqui (shamoonsiddiqui_at_gmail.com)
Date: Sat Nov 14 2009 - 09:56:04 CST
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- Reply: Carlos Simmerling: "Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj"
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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 regardsDr. 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
- application/octet-stream attachment: analyse_hbond.ptraj
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- Previous message: bharat lakhani: "Re: [AMBER] enquiry regarding parameter file to be used"
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