I performed a molecular dynamics simulation for a peptide-receptor complex using the Amber03 forcefield and TIP3 water model. The simulation is convergent in 50ns. Based on the Amber tutorial, using this force field is fine for protein simulation, but based on some references, ff03 is not a standard Amber force field. It's known to provide only an intermediate level of agreement with the experimental data. What are more simulations with the ff03 force field tends to generate ensembles that are distinctly different from other Amber force fields, based on Amber99. [Martín-García, Fernando, et al. "Comparing molecular dynamics force fields in the essential subspace." PLoS One 10.3 (2015).]
I would appreciate it if you would give me your experiences, also some references which used this force field for the all-atom simulation of proteins. Am I need to repeat my simulations?
The AMBER force fields are of the most popularity in current computational biophysics. The preferred rank is AMBER14SB > AMBER99SB-ildn > AMBER99SB ... A new AMBER19SB is also proposed but I would say it behaves similarly with 14SB especially when TIP3P water is used. So no need to update the rank up to now.
According to my experience charmm 27 provides a rational simulations also it can simulate different perspectives related to drug design and discovery whether the disrupting the protein-protein interaction or investigating the stability of protein-protein, protein-peptide or protein-drug interactions.
Dear Najme Dehghanbanadaki
There are 15 force fields in the gmx packages, most of them are good for "globular" protein structure, (what does your protein structure?), I suggest that use OPLS or Amber99sb for globular or kinase proteins.
You can ask if you have any questions.
best
Milad
The AMBER force fields are of the most popularity in current computational biophysics. The preferred rank is AMBER14SB > AMBER99SB-ildn > AMBER99SB ... A new AMBER19SB is also proposed but I would say it behaves similarly with 14SB especially when TIP3P water is used. So no need to update the rank up to now.
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