[gmx-users] Deprotonated Asp and Glu

sun sun.iba2 at gmail.com
Tue May 24 14:31:05 CEST 2016

I have simulated a protein ligand complex and analyzed the trajectory. After visualization of time frames and clusters.pdb; It occurs to me that the Asp and Glu are nit deprotonated although during pdb2gmx I used -inter command and deprotonated both residue according to pH 7. Can anyone tell me if this possible during visualization? or what might the problem be? My protein is Amyloid beta peptide (1-42) and ligand is a small organic molecule (35 atoms), Gromacs 5.0 and ff Gromos96 43A1.
With Regards

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