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Hi, I plan to use “insert-molecules” to add HEPES buffer into the simulation. Justin’s tutorial uses
PRODRG to generate coordinate
gro file and topology
top file. I think I should firstly obtain a PDB of HEPES, where to get it?
Also, I need the HEPES in acid form (protonated) and basic form (deprotonated), how to get them?
In addition, at which stage should I insert the HEPES, is it after
solvate, or adding ions?
Is there a prefered force-field to handle the buffer salt? Now I use amber14sb, is that okay?