Re: [AMBER] checkstructure with cpptraj

From: Daniel Roe <>
Date: Tue, 31 Mar 2020 13:31:51 -0400


On Sun, Mar 29, 2020 at 11:26 AM Nicolas Feldman <> wrote:
> Warning: Action specified before trajin/ensemble. Assuming trajin.

This just means that you told cpptraj to do something (in this case
run the 'checkstructure' action) before telling it what to run on.
Cpptraj can be run on single trajectories or ensembles of trajectories
(e.g. what you would get from a REMD run), and the set up for each is
slightly different.

So the solution is to load a trajectory prior to running 'checkstructure', e.g.:

parm myparm.parm7

Hope this helps,


PS - If you haven't already, you may want to run a few of the analysis
tutorials to become more familiar with cpptraj (or pytraj):

> CHECKSTRUCTURE: Checking atoms in mask '*', warnings output to STDOUT.
> Number of problems in each frame will be saved to set 'CHECK_00001'
> Checking for bond lengths > Req + 1.15 Ang
> Checking for inter-atomic distances < 0.80 Ang.
> Cutoff for building pair list is 4.000000 Ang.
> Do I have to set the protein before loading it to CPPTRAJ ? it is save as .parm7
> Thank you in advance
> Nicolas Feldman
> PhD Student
> The Wellcome-Wolfson Institute for Experimental Medicine
> Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
> _______________________________________________
> AMBER mailing list

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Received on Tue Mar 31 2020 - 11:00:02 PDT
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