[gmx-users] Deprotonated Asp and Glu

[sun]

Allright Thank you very much for quick response. 

Sent from my iPhone

> On 24-May-2016, at 6:05 pm, "Smith, Micholas D." <smithmd at ornl.gov> wrote:
> 
> 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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