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.O
acceptor mask :1-40.N
acceptor mask:1-40.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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Received on Wed May 20 2009 - 13:28:34 PDT
