Hi,
The program is ptraj.
In your case, You could put all your commands in a file, name it "polyAT_vac_md1_12Acut.calc_rms", then run
ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms
Iccy
> Date: Thu, 2 Apr 2009 14:58:47 -0400
> From: pdpatel.mail.ucf.edu
> To: amber.ambermd.org
> Subject: [AMBER] Error in trajin and rms
>
> 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
>
>
>
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Received on Fri Apr 03 2009 - 01:17:00 PDT
