AMBER Archive (2009)

Subject: [AMBER] hbond-error in amber9

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Apr 29 2009 - 21:09:17 CDT


Dear Amber !

I am trying to do hbond
using ptraj in amber 9

mine is a DNA having 1-40 bases

i gave my input file script as
-----------------------------------
trajin tmd_jun.mdcrd
donor mask :1-40_at_O
acceptor mask :1-40_at_N
acceptor mask:1-40_at_H
hbond distance 3.2 angle 120.0
----------------------------------------------

and wen i run it
by giving
$AMBERHOME/exe/ptraj hbond.in

its giving the message
----------------------------------------------
  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 9.0 integrated" (April 2006)
  -/- Executable is: "/home/programs/AMBERHOME/amber9/exe/ptraj"
  /-\
  \-/ Error scanning a value: parm->NTOTAT
Error scanning a value: parm->NTYPES
Error scanning a value: parm->NBONA
Error scanning a value: parm->NTHETH
Error scanning a value: parm->NTHETA
Error scanning a value: parm->NPHIH
Error scanning a value: parm->NPHIA
Error scanning a value: parm->JHPARM
Error scanning a value: parm->JPARM
Error scanning a value: parm->NEXT
Error scanning a value: parm->NTOTRS
Error scanning a value: parm->MBONA
Error scanning a value: parm->MTHETS
Error scanning a value: parm->MPHIA
Error scanning a value: parm->MUMANG
Error scanning a value: parm->MPTRA
Error scanning a value: parm->NATYP
Error scanning a value: parm->NHB
Error scanning a value: parm->IFPERT
Error scanning a value: parm->NBPER
Error scanning a value: parm->NGPER
Error scanning a value: parm->NDPER
Error scanning a value: parm->MBPER
Error scanning a value: parm->MGPER
Error scanning a value: parm->MDPER
Error scanning a value: parm->IFBOX
Error scanning a value: parm->NMXRS
Error scanning a value: parm->IFCAP

ERROR in safe_malloc: Error in alloc of -943208560 bytes

------------------------------------------

is it a error or am i doing mistake ,

regards
balaji
UOM

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