I want to get the psi and phi angles on a particular residue and plot them on ramachandran plot. I went through some tutorials and was informed to use ndx file for that. But can someone give me an actual command to do so.
I use AMBER for my bilayer simulation. I have written FORTRAN 90 code to generate 3 columns and used gnuplot to plot the ramachandran diagram for dihedral angle. If you wish to alter the FORTRAN 90 code then I shall give it to you.
I have 280 aa protein in water as a solvant. I have used GROMACS for simulation. I know i can use g_rama for plotting Ramachandran plot, but I want it to plot only for a particular amino acid (say: tyr 290) not entire protein residues.
Dear Atul,
it looks like VMD may help you. It supports most of popular file formats (including those from GROMACS) and has many built-in tools for MD analysis. The Ramachandran plots plugin which you can find there allows to make a custom selection. It's really nice working and easy to use piece of software, an absolute must-have for me (I'm sure you'll find there a lot of interesting analysis plugins).
Good luck :)
i think you can use VMD as you have to just click the atoms to get the value of dihedral angle for any 4 atoms....and since you have to use only for a single amino acid then its relativily easy..
- Badges
- Science topic