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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of sun <sun.i...@gmail.com> Sent: Tuesday, May 24, 2016 8:33 AM To: gmx-us...@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.i...@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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
