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 Thu Apr 22 2010 - 21:00:02 PDT
