How we could calculate the range of phi and psi angle between a monopeptide.

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Sarang Mahajan

Hey,

I don't know whether there is any software for this. But I used plane geometry to solve similar kind of problems. You have co-ordinates for each atom, you can find the equation of lines connecting these atoms and hence equation of planes consisting of these lines. Phi and Psi angles are just di-hedaral angles between these planes.

Thanks!!

Alessandro Contini

I don't know if I understood your question correctly. I would do an MD (or even a monte carlo search, if the peptide is very small) and then extract the phi and psi dihedrals from the trajectory.

Matthew James Conroy

In your attached file there is no 'range of phi and psi angles'. For a di peptide you can only measure one phi and one psi since both angles are measured across the peptide bond. Several molecular graphics packages will allow you to measure individual dihedrals manually.

It might be helpful to know why you want to do this.

Saugata Hazra

Thanks everyone for your answers.

Prof. Contini, I guess that would be a nice idea to try out. I would let you know about the further proceedings.

Sarang Mahajan: You are absolutely correct about defining the angle phi and psi and measuring them. But my problem is to measure the allowance of phi/psi in a peptide. So, it would be the range of phi and psi and not one particular value of those di-hedral angles.

Dr. Conroy: I guess there is a miscommunication. My file represent a static co-ordinate representing a peptide bond. So, that definitely represent a certain phi or psi. I was asking help/suggestion if it is possible to measure the phi and psi angles for all possible sterically allowed conformation of that peptide. I'm trying to develop a correlation between adopted restriction in a peptide with addition of new amino acid to the structure. Hope it would be clear.