difference between OPLS3 and OPLS4, amber 14sb and amber19sb forcefields

-

 OPLS (Optimized Potentials for Liquid Simulations) and AMBER (Assisted Model Building with Energy Refinement) force fields are widely used in molecular dynamics simulations.


OPLS3 and OPLS4 are the third and fourth versions of the OPLS force field, respectively. The main difference between OPLS3 and OPLS4 is the addition of new dihedral angle parameters in OPLS4, which allow for a more accurate description of torsional profiles. OPLS4 also includes improved electrostatic parameters, including an updated partial charge model and more accurate Lennard-Jones parameters.


AMBER 14SB and AMBER19SB are both versions of the AMBER force field. The main difference between AMBER 14SB and AMBER19SB is the incorporation of updated protein backbone and side-chain torsional parameters, which were derived from quantum mechanics calculations. AMBER19SB also includes updated electrostatic parameters, including the use of the AM1-BCC partial charge model.


Overall, OPLS4 and AMBER19SB are more recent and incorporate more accurate parameters than their earlier counterparts (OPLS3 and AMBER14SB). 

However, there are also some key differences between these force fields:


  • Parameterization: OPLS4 was developed using a combination of quantum mechanical calculations and experimental data, while AMBER19SB was developed primarily using quantum mechanical calculations. This means that the torsional parameters in OPLS4 were derived from both experimental and theoretical data, whereas those in AMBER19SB were derived entirely from theory.
  • Partial charge model: Both force fields use partial charges to describe electrostatic interactions between atoms. OPLS4 uses a standard charge model in which partial charges are derived from ab initio calculations, while AMBER19SB uses the AM1-BCC method to derive partial charges, which can be more accurate for large biomolecules.
  • Water model: Both force fields include a water model to describe solvation effects. OPLS4 uses the TIP4P/2005 water model, while AMBER19SB uses the TIP3P water model.
  • Lipids: OPLS4 includes parameters for lipids, while AMBER19SB does not. This makes OPLS4 a better choice for simulating lipid bilayers or other lipid-containing systems.


Overall, both OPLS4 and AMBER19SB are highly accurate force fields that have been extensively validated in simulations of biomacromolecules. The choice between the two depends on the specific system being studied and the research questions being addressed. It is always important to carefully choose and validate a force field before using it for simulations.

Comments

Post a Comment

Popular posts from this blog

Calculation of RMSD values between two ligand poses using web servers/tools

-
#Web servers for calculation of RMSD values between a ligand poses.  Please note: One pose should be a reference pose and another should be a query pose. PLDbench:  The RMSD value between two molecules can be calculated using PLDbench. There are four modules in this webserver. Single: This module's functionality is limited to calculating RMSD for the 57 complexes utilized in the benchmarking study. Users must submit the docked pose of a ligand that corresponds to one of the 57 PDB-IDs offered in the drop down option in this module. It accepts three file formats: '.pdb', '.mol2', and '.sdf'. Users can choose the type of RMSD they want to compute. Standard heavy-atom RMSD, Hungarian (symmetry-corrected) heavy-atom RMSD, and Minimum-distance heavy-atom RMSD can all be calculated using this module. As a result, the Hungarian (symmetry-corrected) heavy-atom RMSD value is returned by default.  Link for the server:https://webs.iiitd.edu.in/raghava/pldbench/single.p...
Read more

AMBER TUTORIAL-2: How to simulate a protein- ligand system: basic steps for md simulation in amber (AMBER 16)

-
BLOG #3  Hi Guys,           This is a new tutorial on how to simulate a protein-ligand system: basic steps using AMBER. Before we begin, I hope you have read our previous post on AMBER TUTORIAL-1, since I will only be providing additional information with the ligand here, rather than repeating the previous instructions. #To parameterize the ligand file, we start with Antechamber and then parmchck.  These are a series of tools for creating files for organic molecules and some protein metal centers, which can then be read into LEaP. Junmei Wang created the Antechamber suite, which is intended to be used in conjunction with the general AMBER force field (GAFF) (gaff.dat). This is the package's most crucial program. It can convert a variety of files and assign atomic charges and types to them as well. Sqm (or, alternatively, mopac or divcon), atomtype, am1bcc, bondtype, espgen, respgen, and prepgen are among the programs that antechamber runs in respo...
Read more

Python script to plot 3D FEL plots

-
Image
  # To plot FEL in 3D use this python script and run as python2.7 fel3d.py. Here the file uses gibbs.txt. therefore before running the script make sure u have the gibbs.txt in the same folder of this script or else provide the location of the script.  I have attached some images from my research article using the same script for 3D FEL plot These plots are published in  Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1 The 2D FEL scripts are also mentioned in the next blog:  Python script to plot 2D FEL Another point to consider is: when u r plotting FEL plots for multiple systems, make sure your color bar/gradient should be same in all the plots. So u can  change the values in vmax,  ax.set_zlim(0, 18),  ticks=range(0, 21, 2)) in the script below.  Like in my case the highest value was 18 in gibbs free energy (the z axis) in all the axis. therefore i mentioned 18 there...
Read more