RE: AMBER: Could not open file (trajin) with mode (r)

From: Vineet Pande <>
Date: Wed, 23 Mar 2005 16:26:06 +0000

>During one of tutorials when i could do that
>ptraj trajin polyAT_vac_md1_12Acut.mdcrd rms first mass out
>poluAT_vac_md1_12Acut.rms time 0.1 i have msg
>Amber8 Module: ptraj
>Could not open file (trajin) with mode (r)
>ERROR in ptrajInitializeState(): Attempting to open parameter/topology file
>traj in ..
>I thought that was read mode not set to taht file but it wasnt that .

>What i have wrong ??
All the script and input is wrong....there is no topology file indicated.

You should make a separate file... name it anything, say rmsin and in that
file you should have contents which are commands to ptraj, like trajin .....
and trajout ......see the tutorial again carefully. Then in command line
write ptraj prmtop_file < rmsin
that should work
You could also do all this in a single shell script.

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Received on Wed Mar 23 2005 - 16:53:00 PST
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