GROMACS version: 2018.1
GROMACS modification: No
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I have performed an MD on a protein consisting of the A and B chains. I calculated potential energy for AB complex and individual A and B fragments, and then I calculated the: dPE=PEAB-(PEA+PEB). Is it a meaningful quantity for interaction energy between A and B fragments?
If the force field was parametrized in such a way that this quantity is meaningful, yes. Most force fields do not explicitly target such quantities, but some (e.g. CHARMM) do balance all nonbonded interactions against water interactions.
Thank you jastin,
what about other energy terms such as kinetic, total energy, LJ potential and … . is there any reference for interpretation of different energy terms?
Not really. Kinetic energy is directly related to the temperature, the other quantities are entirely force field-dependent and are not necessarily physical.
I am working on the protein-ligand interaction using the procedure proposed by Jastin. I faced two errors:
1- the quality of generated topology for ligand (GEO) by CGenFF server is very low, some penalty values are above 100. How can I fix it?
2- Running gmx grompp for adding ions, I faced 3 equal errors:
ERROR 1 [file geo.prm, line 59]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
Any comment please.
The CGenFF paper discusses how to refine parameters in the event of high penalties. The article is itself a case study/tutorial.
As for the repeated parameters, this issue comes up all the time on this forum. Delete the offending lines from the .prm file. It comes from a version mismatch between the CGenFF server and the force field port. The server is outdated with respect to the current force field.
Thank you justin
I optimized ligand structure using the quantum chemical method in the Gaussian03 program (B3LYP/6-32G). The topology file for this molecule generated by CGenFF server is almost good. All penalties are below 36, except for a dihedral angle containing F atom. Is it good enough for simulation? or it has to be better?
Thanks again.
Penalties below 10 are adequate. If they are 10 - 50, you need to perform basic validation (water interactions and molecular dipole moment for charges, 1-D torsional scans for dihedrals, vibrational frequency analysis or three-point scans for bonds and angles). Anything over 50 shouldn’t be trusted.
Note that you shouldn’t be using DFT for CHARMM/CGenFF parametrization. The force field uses MP2/6-31G* for geometry optimizations and dipole moments, HF/6-31G* for water interactions, and RIMP2/(aug)-cc-pVTZ energies for conformational scans.