GROMACS version:2020
GROMACS modification: No
Here post your question
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 pdb2gmx, editconf, solvate, or adding ions?
Is there a prefered force-field to handle the buffer salt? Now I use amber14sb, is that okay?
You can take pdb for HEPES from a pdb databank (alone or in complex with a biomolecule for example) And/Or you can build the molecule using a visualization software (some visualization softwares have the option to build molecules or fragment of molecules) and save as pdb.
choose force field parameters that are in line with the force field you used to describe rest of the system (in your case amber14sb, as far as I understood)
I assume you want to simulate a biomolecules in HEPES and you have the coordinate file and topology file (itp file) for HEPES in the appropriate protonation form. I suggest the following step
pre-processing of the biomolecule (pdb2gmx)
box definition and solvation of biomolecule (gmx editconf gmx solvate)
insert HEPES molecules (and include the corresponding itp file in the topol.top.
Should I insert-molecules for the acid form (protonated, 0 charge) and basic form (deprotonated, -1 charge) of the HEPES separately? How can I prepare the deprotonated HEPES?
Hi,
Yes, you can insert one type of molecule at the time.
You can manually build the deprotonated form, or use a graphical software that allows to delete atoms
Best regards
Alessandra