Hello Dan,
Thank you very much.
I saw some of the tutorials and did others. Maybe my second question after your email will be: If I want to check if there is any overlap or clash between aminoacid while doing minization/equilibration of the system and I want to use checkstructure or checkoverlap how can I set the input that I want to run over my protein or there is any input already loaded in CPPTRAJ ?
Nicolas Feldman
PhD Student
The Wellcome-Wolfson Institute for Experimental Medicine
Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Tuesday, March 31, 2020 6:32 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] checkstructure with cpptraj
This message is from an external sender. Please take care when responding, clicking links or opening attachments.
Hi,
On Sun, Mar 29, 2020 at 11:26 AM Nicolas Feldman <nfeldman01.qub.ac.uk> 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
trajin mytraj.nc
checkstructure
Hope this helps,
-Dan
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):
https://ambermd.org/tutorials/TrajectoryAnalysis.php
> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 31 2020 - 11:30:02 PDT
