Hello researchers,
I have processed a MD simulation study of 26 amino acid amylose chain in water using gromacs. Now i want to analyze Dihedral angle for the glucose residues alpha 1-4 linkage, defined by atoms O5-C1-O4'-C4' (phi) and C1-O4'-C4'-C3' (psi).
I tried generating angular index file for dihedral angles, showing various phi angles. I also tried also check various publication but none of them have mentioned the methodology to calculate dihedral angles.
Please help me with the calculation of dihedral angles.
Thank you in anticipation.
Build your system with moltemplate, I have always used it and its generate the dihedrals angles.
one other choice is to use swissparm but this will be long path and takes time to do it manually.
Noor Alomari,
Thank you for your response.
I have completed the 100ns simulation using gromacs under charmm force field.
How am i supposed to process this MDS for dihedral angle calculations.
Pawan,if your simulation is done then use Vmd to calculate dihedrals VMD, enter the pick dihedral mode by pressing 4 . This mode allows you to select four atoms involved in the dihedral angle you want to analyze. VMD will then display labels for each of these atoms, along with the corresponding dihedral angle value.
Thank you Noor Alomari ,
I got the dihedral angles using the VMD module after pressing 4. But i want to analyze the dihedral angles (PHI and PSI), throughout the simulation.
Please guide something.
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