[gmx-users] Deprotonated Asp and Glu

Smith, Micholas D. smithmd at ornl.gov
Tue May 24 14:36:00 CEST 2016

Best thing to do would be to check the *.gro and *.top files and see if it really is deprotonated.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of sun <sun.iba2 at gmail.com>
Sent: Tuesday, May 24, 2016 8:33 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Deprotonated Asp and Glu

The charge on Asp amd Glu seems 0 and hydrogens are present in time frames and cluster.pdb. But I deprotonated during pd2gmx.

Sent from my iPhone

> On 24-May-2016, at 6:00 pm, sun <sun.iba2 at gmail.com> wrote:
> Hello
> 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
> Suniba
> Sent from my iPhone
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