AMBER Archive (2008)

Subject: Re: AMBER: How to convert a CHARMM trajectory to AMBER format?

From: Wei Huang (whuang_at_cct.lsu.edu)
Date: Tue Aug 19 2008 - 09:02:22 CDT

Hi Jeffrey,

What's the format of your psf file? It should be a CHARMM format psf
file.

Cheers,
Wei
On Tue, 2008-08-19 at 19:30 +0800, Jeffrey wrote:
> Dear all,
>
> I am new to amber. So could someone please tell me how to convert a md trajectory generated in CHARMM to AMBER format? I write the following script.amber, but it doesn't work...
> ----
> ptraj prot0-10090.psf << EOF
> trajin orient0-10090prot.dcd 1000 10090000 1000
> trajout amber.traj
> EOF
> ----
>
> When run the script by "ptraj script.amber", the following message was displayed:
> ---
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 9.0 integrated" (April 2006)
> -/- Executable is: "ptraj"
> /-\
> \-/ Error scanning a value: parm->NTOTAT
> Error scanning a value: parm->NTYPES
> Error scanning a value: parm->NBONH
> Error scanning a value: parm->NTHETH
> 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->MUMBND
> Error scanning a value: parm->MUMANG
> 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 in NAME_COPY: ... EOF encounters on scanning igraph
> ----
>
>
> Any suggestion is greatly appreciated.
> Thanks very much for the time.
>
> Have a nice day.
>
> -------
> Jeffrey
>
>
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-- 
Graduate Research Assistant
224 Johnston Hall
Louisiana State University
Baton Rouge, LA 70803
Tel. (225)252-0034
E-mail: whuang_at_cct.lsu.edu
Web: http://www.cct.lsu.edu/~whuang

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