Hello,
I'm attempting to get an analysis of side-chain to side-chain hydrogen
bonding in ptraj from an MD run on a protein of 114 residues. Its
aborting and I'm guessing due to a memory issue, but I'd like any help to
see if its something wrong with my input file. Thanks in advance!
Jamie
***The output I'm getting is:
PTRAJ: strip :WAT
Mask [:WAT] represents 12831 atoms
PTRAJ: center :0-114
Mask [:0-114] represents 1875 atoms
*** glibc detected *** ptraj: double free or corruption (out):
0x000000000083efc0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x38d6271684]
/lib64/libc.so.6(cfree+0x8c)[0x38d6274ccc]
ptraj[0x41daae]
======= Memory map: ========
followed by an extensive listing.
***My input file is as follows:
#ptraj file for side-chain to side-chain hydrogen bonding data
#read in file coordinates from end of isochoric and isobaric processes
trajin Isobaric10ns.mdcrd.gz
#Strip all water molecules, leaving just the protein (solute)
strip :WAT
#Center the geometry of the residues listed to the origin
center :0-114
image origin center
#--Now to add in the hydrogen bonding options, (occuring between backbone
oxygens and amide hydrogens)
#-- 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 :ASH.OD1
donor mask :ASH.OD2
donor mask :GLU.OE1
donor mask :GLU.OE2
donor mask :GLH.OE1
donor mask :GLH.OE2
donor mask :SER.OG
donor mask :THR.OG1
donor mask :HIS.ND1
donor mask :HIE.ND1
donor mask :HID.NE2
donor mask :HIP.ND1,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
#hbond command options
hbond distance 3.5 angle 60.0 solventneighbor 6 print 0.05 series hbt out
hbond.out
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Received on Wed Mar 17 2010 - 15:00:03 PDT
