normal How the pH is reflected in the martini?

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2 months 6 days ago #7994 by lanselibai
How the pH is reflected in the martini? was created by lanselibai
I want to simulate a protein at pH 4. In the all-atom MD, I interactively assign the protonation states to individual chargeable residues, based on the pdb2pqr server
nbcr-222.ucsd.edu/pdb2pqr_2.1.1/

So how these protonation states could be reflected in the coarse-grained models?

The "-his" can be used for the histidines, but how about the others?

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1 month 2 weeks ago #8021 by lanselibai
Replied by lanselibai on topic How the pH is reflected in the martini?
Change the five chargeable residues in the itp file generated by martinize.py, based on the amino acid itp files at www.cgmartini.nl/index.php/force-field-parameters/amino-acids

e.g.
mailman-1.sys.kth.se/pipermail/gromacs.o...-January/124004.html

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