Hi
I am trying to run the MD simulation for protein-ligand system in NAMD. But I am having troubles running it. It says the ligand is not parametrised when generating psf file.
I understood the protein and ligand pdb files should be prepared separately, where the ligand is parameterised and combine it to form pdb of the complex.
Can any one give me detailed explanation how to do the MD simulation for protein-ligand complex in NAMD or suggest a good tutorial to do that?
I am very new to MD things, but I eventually figured out to run the MD simulation for the protein alone in NAMD.
You can try CGenFF program to generate the force field parameters http://mackerell.umaryland.edu/cgenff_indx.php
you can upload your complex at http://www.charmm-gui.org/?doc=input ; PBD reader it will provide the required parameters for both protein and ligand. but first you have to edit your PDB file of the complex in a way that your ligand atoms is the continuation after the last atom of your protein and the same for residue number; assign your ligand with a number after the last residue of your protein. One last detail, assign the ligand with different chain number; i.e, if your protein chain in A, you may assign "X" for your ligand to be read by charmm gui.
good luck
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