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I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have written a code for the backbone alone (i.e) to construct cartesian coordinates of each atom in backbone from the respective internal coordinates(without side chains). However I got to know that this can be done in a software (maybe in PyMol or VMD). I am completely a beginner in this field of biochemistry/bioinformatics/biophysics. Does it really possible to do this in software like PYMOL/VMD? I'll be very happy if I can do this in python itself. I want to generate cartesian coordinate of a given tetrapeptide for all possible Ramachandran angles (within the allowed region)

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  • $\begingroup$ Do you have the structure of the tetrapeptide provided or you want to run a simulation and get all the possible dihedral angles (they are not called Ramachandran angles)?. $\endgroup$
    – Roni Saiba
    Nov 28, 2020 at 7:09
  • $\begingroup$ No, I have just bond angles, bond lengths (standard values). Now for a given set of dihedral angles (Ramachandran angles) for tetrapeptide I need to generate the cartesian coordinates. I need to simulate the structure. I don't want the minimum energy structure. I just want to get the structure of tetrapeptide for a given set of internal coordinates ). @RoniSaiba $\endgroup$ Nov 28, 2020 at 7:43
  • $\begingroup$ VMD by itself can't generate MD trajectories. You will need some other software like NAMD or the like to do so. However, once you have a trajectory, you can write a script (in Tcl) for VMD which will give you the cartesian coordinates of the atoms in a txt file which you can then process in python, R etc. Here is a Tutorial on how to use NAMD and VMD to get the job done. You will have to first make a .PDB of your tetrapeptide. You can use Avogadro to do that. $\endgroup$
    – Roni Saiba
    Nov 28, 2020 at 12:46
  • $\begingroup$ Is it a biology or bioinformatics STACK forum question ??? It could be also a chemistry one if talking about molecular dinamics ?? A penny for your thoughts $\endgroup$
    – pippo1980
    Aug 25, 2022 at 15:34

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