Is it possible to do MD simulation on Metalloproteins (specifically with Mg) with gromos force filed? And if yes, could you please explain what are the requirements? I would be glad if some one who has the same experience, give me some detailed information.
Visit the following websites:
https://atb.uq.edu.au/
http://zarbi.chem.yale.edu/ligpargen/
Check Table 1 here.
https://www.ncbi.nlm.nih.gov/pubmed/30521334
Basically you can take the parameters (of your choice) from AMBER and update ffnonbonded.itp.
Yes, Gromos FF has parameters for ion Mg(2+).
What kind of information do you need? what software do you intend to use?
This article may help you.
Article Interactions of cantharidin-like inhibitors with human prote...
What I mean is what is the parameters for "coordinated Mg" for gromos 54a7, for example? The only file I have to change is ffnonbonded.itp or not?
- Badges
- Science topic
- Similar topics
- Filing