AMBER Archive (2009)
Subject: Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj

From: shamoon siddiqui (shamoonsiddiqui_at_gmail.com)
Date: Sat Nov 14 2009 - 10:19:04 CST

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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_at_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_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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- With best regards

Dr. Shamoon Ahmad Siddiqui DBT Postdoctoral Fellow Molecular Biophysics Unit Indian Institute of Science Bangalore-560012, India

application/octet-stream attachment: analyse_hbond.ptraj

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Previous message: Carlos Simmerling: "Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj"
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AMBER Archive (2009)Subject: Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj

AMBER Archive (2009)
Subject: Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj