I have a protein-peptide complex that I would like to run an MD simulation on and I'm using the parameters that I got from a paper. The majority of parameters are quite clearly laid out in the paper but I'm struggling with position restraints for the protein-peptide complex.
I understand what position restraints are/what purpose they serve, but can anyone please explain to me where to get the values for position restraints? The paper I'm using merely states, "using Nose-Hoover thermostat with position restraints for the protein-peptide complexes."
Are they "standard" for protein-peptide or protein-ligand systems? Do you get them by trial and error? Are they system-specific? Does the forcefield automatically apply/determine them?
I managed to find some restraints "-DPOSRES_FC_BB=400.0 -DPOSRES_FC_SC=40.0" in a tutorial simulation file, but I'm not sure what they mean. Please help?
Hi, when you generate the topology using gmx pdb2gmx, gmx automatically generates the position restraints file for each protein chain and they are normally named as "posre_chainX.itp" or something similar name.
During NVT (temp equilibrium) and NPT (pressure equilibrium), you need to mention a keyword in mdp file "-DPOSRES" something like this:
define = -DPOSRES ; position restrain the protein
I recommend you to read and follow this tutorial by Prof. Justin.
Lysozyme in Water (mdtutorials.com)
It will give you good idea and basics of gromacs. Since, your system is protein-peptide that is in principal "protein in water" so you don't need to change anything.
Hi Ayaz Anwar thank you so much for your response.
I have gone through both the Lysozyme in Water and Protein in Water GROMACS tutorials, and they helped a lot in understanding the steps and explaining each part. But I'm preparing my system with CHARMM-GUI, so would my position restraints also simply be generated by CHARMM-GUI as gmx would if I used pdb2gmx? Would I need to change anything because I'm using CHARMM-GUI?
I never used CHARMM-GUI but I hope it should have some option to generate the posre files. Otherwise, since you are dealing with GMX, there is one more tool in gmx, gmx genrestr that can generate this file.
gmx genrestr — GROMACS 2018 documentation
Please read the help file for input and output, it is easy. Then you can proceed with your simulation.
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