AMBER Archive (2009)

Subject: [AMBER] Error in trajin and rms

From: Pansy Patel (
Date: Thu Apr 02 2009 - 13:58:47 CDT


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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