Guessing dihedrals for Ramachandran plots

Dear all,

I asked a question a while ago and it went unnoticed; my problem is to get dihedrals from a lammps dump file (attached) that does not have them by using the “topo guessdihedrals” command and then perform ramachandran analysis on the structure. I am sure I am doing something wrong but i could not find a clear answer to this after working through all the tutorials. Ramachandran plots seem to show just one peak in the middle…

Please find attached an example of my lammps dumpfile that I wish to analyse. What I do is wrong but I do not know what the issue is…There was not much about how the dihedrals are read exactly in Ramachandran plots in vmd so I could not really read up on that…

Thank you for your time & best wishes


deform_nve.dump.150000 (37 KB)