What do you mean by similar?
ptraj performs a dynamic analysis, so on the course of the simulation many
things can happen. It would be helpful if you could clarify the details of
your simulation as well as what you claim that is wrong with the results.
The script looks fine for me.
On Sun, Sep 25, 2011 at 11:30 PM, qiao xue <xueqiaoup.gmail.com> wrote:
> Hello all,
>
> When I took Hbond calculation with Amber I suffered some problems.
>
> The moleculars are a monomer and a dimer, I think many hbonds of them
> should be similar more or less. But the results are very different.
>
> the hbond.ptraj of monomer is this:
> trajin md.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
>
> #-- 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
>
> #-- 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 :3-10,12-23,25-42,44-85,87-101,103-112,114-124,126-127.N:2-127.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
>
>
> And the hbond.ptraj of dimer is this
> trajin md.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 :AS4.OD1
> donor mask :AS4.OD2
> donor mask :GL4.OE1
> donor mask :GL4.OE2
> donor mask :SER.OG
> donor mask :THR.OG1
> donor mask :HIP.ND1
> donor mask :HIP.ND1
> donor mask :HIP.NE2
>
> #-- 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 :HIP.NE2 :HIP.HE2
> acceptor mask :HIP.NE2 :HIP.HE2
> acceptor mask :HIP.ND1 :HIP.HD1
> acceptor mask :HIP.ND1,NE2 :HIP.HE2,HD1
>
> #-- 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
> :3-10,12-23,25-42,44-54,56-85,87-101,103-112,114-124,126-127,128,130-137,139-150,152-169,171-181,183-212,214-228,230-239,241-251,253-254.N
> :2-254.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
>
>
> My question is that what should be modified of the script when taking
> hbond analysis of dimer?
> Or just treat the dimer like a usual molecular?
>
> Thanks
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Sep 26 2011 - 06:00:04 PDT
