AMBER Archive (2009)

Subject: Re: [AMBER] Error in trajin and rms

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Apr 02 2009 - 14:19:39 CDT

these are ptraj commands nout unix ones, so these go inisde a ptraj input file.

On 4/2/09, Pansy Patel <pdpatel_at_mail.ucf.edu> wrote:
> Hello
>
> I am trying to run the tutorial b1 section 3
> The Md runs successfully with both vacuum and implicit solvent
>
> However, when I typed the commands to run trajectory the following error
> messages appeared,
> I can find the ptraj file in the exe directory, but not trajin and rms.
>
> [PATH]$ trajin polyAT_vac_md1_12Acut.mdcrd
> bash: trajin: command not found
>
> [PATH$ rms first mass out polyAT_vac_md1_12Acut.rms time 0.1
> bash: rms: command not found
>
> [PATH]$ ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms
> bash: polyAT_vac_md1_12Acut.calc_rms: No such file or directory
>
> Can somebody tell me what I am doing wrong?
>
> Best regards,
>
> Pansy D Patel
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
Stony Brook University           E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber