Re: [AMBER] Extract trajectories REMD

From: Juliette Newell via AMBER <>
Date: Wed, 15 Jun 2022 09:40:59 +0000

Hi Dan,

Thank you for getting back to me.

I have had a look at the cpptraj manual and also the replica exchange tutorial on the amber MD website and I am unsure where I am going wrong.

The example in the manual says :

trajin rem.001 remdtraj remdtrajtemp 300

will this loop over all replicas? Or will I have to change the temperature at the end.

Or the second example is:

trajin rem.001 remdtraj remdtrajtemp 300 trajnames rem.002,rem.003,rem.004

but this will require manually typing out all of the individual replicas

And I have set the extenstion similarly to the tutorial which is :

set i = "1"
while ($i < 8)
set ext=`printf "%3.3i" $i`

I have changed < 8 to reflect my system, but i still get the same error.

Thanks for your help,


From: Roe, Daniel (NIH/NHLBI) [E] <>
Sent: 14 June 2022 15:00
To: AMBER Mailing List <>
Subject: Re: [AMBER] Extract trajectories REMD


> the error message I get is:
> Error: Unrecognised variable in command: i
> [trajin remdtraj remd.mdcrd.printf "%3.3i" $i]
> Error: 'remd.mdcrd.printf': No such file or directors
> Error: Could not set up input trajector 'remd.mdcrd.printf'.

There is an error in your script. You're assigning the 'ext' variable incorrectly, so the file name that gets passed to trajin is "remd.mdcrd.printf "%3.3i" $i". You need to fix your script and assign 'ext' properly.

>for T in $TEMPLIST ; do
> cpptraj
> trajin remd.mdcrd.001 remdtraj remdtrajtemp $T
> trajout remd.Ttraj.$T

This is incorrect - you shouldn't be doing a loop for 'remdtraj'; you specify the "lowest" replica, and cpptraj automatically searches for the remaining trajectories based on extension. Alternatively you can specify the remaining trajectories manually with the 'trajnames' keyword. I recommend reading the manual entry for 'trajin'; there is a subsection on how to use the 'remdtraj' keyword.

Hope this helps,

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Received on Thu Aug 04 2022 - 13:30:25 PDT
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