I have some protein-ligand complex to simulate on GROMACS version:unchecked. For preparation of my ligands, I submitted the extracted Ligand.pdb file and submitted it in the Prodrg server, Energy Minimisation was nullified. In the output zip folder I had my ITP file and I encountered 5 PDB files, names mentioned above. Which of the PDB file do I need to keep for further simulation?
Debanjan Kundu Please read the manual for the .itp files of ligand used in gromacs.
Try DRGAPH.PDB as well as the DRGAPH.GRO file. This will have the most accurate number of coordinates.
Try using ATB server instead of ProDrg server as it doesn't generate more accurate parameters. You can even try latest Gromacs tutorial by Dr. Justin to use Charmm ff and parameters
Thank you Dr Thirumal Kumar D & K. Venkateswara Swamy for your suggestions!
Dear Debanjan Kundu,
Pls, focus on the DRGAPH.PDB and DRGAPH.GRO files and rename them accordingly. And follow the tutorial from Dr. Justin Lemkul.
I would strongly suggest you try Charmm ff from CGenff for protein-ligand molecular dynamics.
All the best!!
You need the DRGAPH.GRO and the itp file for your simulation. There is a readme file among the outputs which will give you details about the generated files. Refer to the Beevan lab tutorial.
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