these are ptraj commands nout unix ones, so these go inisde a ptraj input file.
On 4/2/09, Pansy Patel <pdpatel.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
>
>
>
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Received on Fri Apr 03 2009 - 01:17:02 PDT
