Error in alloc of - 1216928392 bytes
this is due to memory.
On Thu, Apr 22, 2010 at 10:54 PM, geyan <geyan.big.ac.cn> wrote:
> identical with the tutorial but with error output message?make sure all the
> input file is correct especially the trajectory,which seems have some
> mistake from the error message.
>
>
> 2010-04-23
>
>
>
> geyan
>
>
>
> 发件人： Yunfen Wang
> 发送时间： 2010-04-23 11:31:25
> 收件人： amber
> 抄送：
> 主题： [AMBER] H-bond analysis in ptraj
>
> Hi all,
> I am doing H-bond analysis of pr with solvent in order to see the solvent
> effect on pr . But when I did ,it just ran a short time , showing that :
> checking coordinates: equil1-6.binpos
> Error in safe-malloc: Error in alloc of
> - 1216928392 bytes
> The analysis progress is according a example in the amber tutorials .
> The following is the ptraj script:
> analyse_hbond.ptraj
> trajin equil1-6.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 :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
>
> What is wrong with that? My computer is 3.0GHz and 1G memory. Or My
> analysis meaning to is unreasonable? Any help is appreciated .
> sincerly,
> Lisa
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Received on Fri Apr 23 2010 - 00:00:03 PDT
