Hi ahmed,
Thank you I'll try to work my way through.
Kind regards,
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: Ahmed Elrashedy <ahmedelrashedy45.gmail.com>
Sent: Tuesday, March 31, 2020 7:30 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
You input will be as follows
parm parm_water.Parm7
trajin Heating.nc
checkstructure
Thank you and Best regards.
Ahmed Elrashedy
Molecular Bio-computation and Drug Design Laboratory
Discipline of Pharmaceutical Sciences
School of Health Science
University of KwaZulu-Natal
Westville Campus
Private Bag X54001
Durban 4000
South Africa
On Tue, Mar 31, 2020 at 8:08 PM Nicolas Feldman <nfeldman01.qub.ac.uk>
wrote:
> 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
>
_______________________________________________
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 - 13:00:02 PDT
