AMBER Archive (2009)

Subject: RE: [Subject Filtered] [AMBER] hbond-error in amber9 8%

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Thu Apr 30 2009 - 19:02:34 CDT

Hi Balaji,

I've seen this error before when the first line of a .prmtop file is
missing. An example of the first line looks like:

        %VERSION VERSION_STAMP = V0001.000 DATE = 03/30/09 16:34:03

If it appears that this line is missing from your .prmtop file, try
editing in something very similar using an appropriate date (e.g., check
the Leap Log from when you created the .prmtop file if it exists).

It seems that this line is occasionally missing after running one of the
Amber 9 or AmberTools 1.2 programs that I've been using, but I haven't
yet tracked down what is actually happening -- including 'Operator
Error' ;-)

Good Luck,
Bob Hopkins

-----Original Message -----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of balaji nagarajan
Sent: Wednesday, April 29, 2009 9:09 PM
To: amber forumnew
Subject: [Subject Filtered] [AMBER] hbond-error in amber9 8%

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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