Re: [AMBER] Rotation Matrix

From: mohamed marzouk <mohamedmarzoukphysics.gmail.com>
Date: Thu, 21 Oct 2021 23:55:25 +0000

Hello,
Now itís working, the function available in Amber tools 18 not older editions!!!
Thank you

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________________________________
From: mohamed marzouk <mohamedmarzoukphysics.gmail.com>
Sent: Saturday, October 16, 2021 9:00:02 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Rotation Matrix

You need the "matricesout" option. Type "help rmsd" at the cpptraj prompt,
or get a bit more expanded description from the Reference Manual.

I tried matricesout but still not working
The error message !!!

Error: [rmsd] Not all arguments handled: [ matricesout test4[RM] ]

The commands tried
rmsd test1 :1-198&!.H= first out rmsd_first_protein_testmatrices2.agr savematrices matricesout
rmsd test3 :1-198&!.H= first out rmsd_first_protein_testmatrices2.agr savematrices matricesout test.agr
rmsd test4 :1-198&!.H= first out rmsd_first_protein_testmatrices2.agr savematrices matricesout test4[RM]

I am using
CPPTRAJ: Trajectory Analysis. V17.00


Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
 mohamed_marzouk.sci.asu.edu.eg<mailto:mohamed_marzouk.sci.asu.edu.eg>
 marzouk.aa.m.titech.ac.jp<mailto:marzouk.aa.m.titech.ac.jp>
 marzouk_biophysics.yahoo.com<mailto:marzouk_biophysics.yahoo.com>
 mohamedmarzoukphysics.gmail.com<mailto:mohamedmarzoukphysics.gmail.com>

Mob. and WhatsApp.:
               +81 070-4070-9549
                +2 01061417414





On Reiwa 3 Oct 16, at 20:40, David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> wrote:

On Sat, Oct 16, 2021, mohamed marzouk wrote:

I tried savematrices option but it is saved as dataset not output file as in attached photo !!!
rmsd ToFirst :1-198&!.H= first savematrices out rmsd_first_protein_testmatrices2.agr


You need the "matricesout" option. Type "help rmsd" at the cpptraj prompt,
or get a bit more expanded description from the Reference Manual.

...dac


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Received on Thu Oct 21 2021 - 17:00:02 PDT
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