2 votes

How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?

In order to run Molecular Dynamics simulations (independent of the force-field and type of simulation) you need a file with the structure of your protein: type of atoms, residues and (X, Y, Z) ...
Camps's user avatar
  • 23.3k
1 vote

How to use martinize.py?

As per the README we can invoke martinize as follows: martinize.py -i input.pdb -o output.pdb I ran the command on a PDB of 4poj And I get the following output ...
Vandan Revanur's user avatar
1 vote
Accepted

What is the purpose of DSSP when using martinize2?

Just basically collecting the comments here. The tutorials page for Martini states: The secondary structure of the protein influences both the selected bead types and bond/angle/dihedral parameters ...

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