AMBER Archive (2006)

Subject: RE: AMBER: trajin and rms

From: Ross Walker (
Date: Sun May 21 2006 - 23:43:09 CDT

> [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

Create a file called "polyAT_vac_md1_12Acut.calc_rms" and into it put the
commands for ptraj to process. That is:

trajin polyAT_vac_md1_12Acut.mdcrd
rms first mass out polyAT_vac_md1_12Acut.rms time 0.1
> [PATH]$ ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms
> bash: polyAT_vac_md1_12Acut.calc_rms: No such file or directory

Then have ptraj process that list of commands with:

$AMBERHOME/exe/ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms

And it should work.

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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