Hello, I am fairly new to gromacs and molecular dynamics. I want to simulate thiols for starters for some applications and I want to generate the topology file for thiol. I found the PDB and ITP files for sulfanyl from ATB -
https://atb.uq.edu.au/molecule.py?molid=4568#panel-md
and I tried to use ‘pdb2gmx’. I have read up on the documentation but I can’t get it to work. I am stuck on how to modify a forcefield or how to simply create a new one for the molecule. Any help on how to generate the topology and gro files would be appreciated. Thanks
Hi, you already got the topology file (itp), so you don't need topology.
In your case, just create the protein topology using pdb2gmx and then combine it later. YOu should follow this tutorial:
http://www.mdtutorials.com/gmx/complex/index.htmlcreate
Just consider the thiol group as a ligand. If you have downloaded it from the ATB, then, I hope the structure and charges are already optimized.
Good luck.
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