[gmx-users] Ramachandran Plot for a Polymer

Dear Gromacs Users, Can we get the Ramachandran plot for a polymer using Gromacs? If we can, how do we do that? Appreciate your help. Thank you. -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

Re: [gmx-users] ramachandran plot

> Message: 4 > Date: Wed, 9 Jan 2019 11:59:31 +0100 > From: Tamas Hegedus > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] ramachandran plot > Message-ID: <563a0c65-532e-a47d-fdf7-5046a062c...@hegelab.org> > Content-Type: text/plain; chars

Re: [gmx-users] ramachandran plot

> Message: 5 > Date: Wed, 9 Jan 2019 17:17:31 +0530 > From: Subhomoi Borkotoky > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ramachandran plot > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Hii Subhomoi Thank you so much for you

Re: [gmx-users] ramachandran plot

Hi Javed, I hope *gmx rama* will solve the issue. http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* DBT Research Associate, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delh

Re: [gmx-users] ramachandran plot

Hi, I use the python MDAnalysis packages for this. https://github.com/MDAnalysis/mdanalysis/issues/1335 https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html Have a nice day, Tamas On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: Dear Users Can anyone suggest m

[gmx-users] ramachandran plot

Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain priv

Re: [gmx-users] Ramachandran plot

Thank you Dear Mark. Its my pleasure taking your time. ;-) On Wed, Jun 7, 2017 at 2:25 PM, Mark Abraham wrote: > Hi, > > This is why you should actually copy and paste your command lines so you > don't waste your time ;-) And mine. > > Unless you wrote your entire system to your xtc file, your

Re: [gmx-users] Ramachandran plot

Hi, This is why you should actually copy and paste your command lines so you don't waste your time ;-) And mine. Unless you wrote your entire system to your xtc file, your tpr has more atoms than your xtc, and thus probably some more dihedrals. Make a matching subset of your tpr using gmx convert

Re: [gmx-users] Ramachandran plot

Dear Mark Thank you gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg This was my command.. I didn't choose any dihedral particularly On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham wrote: > Hi, > > Sounds like your choice of dihedrals doesn't match your system. How did you > select them? >

Re: [gmx-users] Ramachandran plot

Hi, Sounds like your choice of dihedrals doesn't match your system. How did you select them? Mark On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > Dear Users > > When I try to execute ramachandran plot analysis, I get the following note > like "Dihedral around 5809,5816 not found in topology. Us

[gmx-users] Ramachandran plot

Dear Users When I try to execute ramachandran plot analysis, I get the following note like "Dihedral around 5809,5816 not found in topology. Using mult=3" (nearly 30-40 dihedrals). What is it about? Input is just protein structure extended upto 150ns. -- *Regards,* *Rahul Suresh* *Research Scho

Re: [gmx-users] ramachandran plot

Hi Tsjerk, I was wondering how did you get the input.dat file? did you got it from grace/xmgrace? I was able to save the plot in .ps or .png format file. However whenever I tried to run kde2d.r I was getting an error: Please see below: ./kde2d.r ramachandran.png ramachandran-2.png ./kde2d.r: line

Re: [gmx-users] ramachandran plot

Hi Urszula, Save the following as kde2d.r and make it executable. Then you can run ./kde2d.r rama.dat rama.png Cheers, Tsjerk kde2d.r #!/usr/bin/env Rscript # Script for drawing 2D combined linear/circular KDE plots. # # (c)2014 Tsjerk A. Wassenaar # Friedrich-Alexander Unive

Re: [gmx-users] ramachandran plot

Dear Tsjerk, Could you send me the script again? as I did not find the attachment in your previous email. best regards Urszula > Hi Urszula, > > Attached is an R script for drawing 2D circular or combined > circular/linear > KDEs. It works as a command line script, taking as arguments a file wi

Re: [gmx-users] ramachandran plot

Hi Urszula, Attached is an R script for drawing 2D circular or combined circular/linear KDEs. It works as a command line script, taking as arguments a file with 2-column data, and an output image file name (./kde2d.r input.dat output.png). It's pretty easy to adapt to suit your needs, even if you

Re: [gmx-users] ramachandran plot

Could you please send me the code? It can be on my private email. Thanks a lot Ursuzla > Hi Urszula, > > It's a while ago that I made that one, and I don't have the code at hand. > But it's a combination of a density plot (kde2d) with the points laid > over, > and a polygon to highlight the forb

Re: [gmx-users] ramachandran plot

Hi Urszula, It's a while ago that I made that one, and I don't have the code at hand. But it's a combination of a density plot (kde2d) with the points laid over, and a polygon to highlight the forbidden region. These days I'm doing circular 2D KDEs, whic is more correct. I can send the R code for

[gmx-users] ramachandran plot

Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta w