I have Designed a Ligand candidate which has an organic scaffold and a small peptide chain with 40 Amino Acid residues attached to it through an amide bond. and I want to set up a MD simulation foe this complex. It was unable to create the topology files for this complex. because it was confusing how to create parameters for the amide bond created between peptide and organic structure.
can somebody please advice me on creating the topology file for this complex to start up the MD simulations
Assign proper atomic charges and atom types, and add missing parameters (bonds, bond angles, and torsion angles) by analogy to the parameters already defined in the chosen force field, or borrow them from another force field that is compatible with the chosen one.
There are online servers for example, ATB server, which shall provide you with the gromacs compatible topology files (all-atom/ united atom). After that you can edit the file if you want to specifically tune some interactions. Or you can use antechamber package that comes with AMBER tools to generate the topology for AMBER and later convert it using a simple python script (available online) in gromacs compatible format. You can directly use AMBER for your simulation as well.
Dear Chamikara Herath,
If you intend to use Gromacs package, Automated Topology Builder (ATB) (https://atb.uq.edu.au/) is a excellent choice for generating topology. You will need only the pdb files, with the hydrogen atoms, to get the topologies with the gromos Force-Field.
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