I have performed protonation using Avogadro which is protonating Carboxylate. Can I use chimera/pymol to generate .mol2 file (Not sure if they same as Sybyl)?
If not so, can I delete the “H” entries of caboxylate group manually after converting into SYBYL mol2 in avogadro?
Most programs just fully protonate everything. Just delete the unnecessary proton and generate the .mol2 file.
Hi Sir, @jalemkul
I am also facing the same issue while simulating one heterodime protein in gromacs. The RMSD graph is showing huge fluctuations. Can you please kindly suggest any solutions for this?