AMBER Archive (2009)

Subject: Re: [AMBER] hbond-error in amber9

From: Alessandro S. Nascimento (asnascimento_at_if.sc.usp.br)
Date: Thu Apr 30 2009 - 05:46:02 CDT


try using:

$ptraj XXX.prmtop <hbond.in > mylogfile.log

HTH

--asn

On Wed, Apr 29, 2009 at 11:09 PM, balaji nagarajan
<balaji_sethu_at_hotmail.com> wrote:
>
> 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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-- 
[ ]s

--alessandro

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