Re: [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." <smit...@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-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
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Re: [gmx-users] Deprotonated Asp and Glu

[Smith, Micholas D.]

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
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Re: [gmx-users] Deprotonated Asp and Glu

[Justin Lemkul]

On 5/24/16 8:30 AM, sun 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


The simulation won't do anything you don't tell it.  Asp and Glu are 
deprotonated by default in pdb2gmx, so there should be no need to do anything to 
them.  Probably you made the wrong choice when setting up the topology.  The 
contents of the topology are definitive; if you're seeing unexpected "bonds" in 
a visualization software, those are typically guessed from the coordinates and 
are not necessarily real (e.g. nearby water/ligand H might get "bonded" to an 
Asp/Glu).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Deprotonated Asp and Glu

[sun]

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  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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[gmx-users] Deprotonated Asp and Glu

[sun]

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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