Re: [gmx-users] Fixing periodicity effects on trajectory file

[Justin Lemkul]

On 9/16/15 1:23 AM, Homa rooz wrote:

Dear Justin
​If you asked about verifying docking process​. I should say, I have worked
with single chain protein and the best ranked binding energy was -7.41
kcal/mol by AutoDock 4.2, considering that binding site was located on turn
structure and the edge of protein, seeming unstable. I didn't check the
result by another software.



Then what Michael said is likely true: your ligand dissociated and what you are 
observing is a real effect and not simply a PBC artifact.


-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] Fixing periodicity effects on trajectory file

[Homa rooz]

Dear Justin
​If you asked about verifying docking process​. I should say, I have worked
with single chain protein and the best ranked binding energy was -7.41
kcal/mol by AutoDock 4.2, considering that binding site was located on turn
structure and the edge of protein, seeming unstable. I didn't check the
result by another software.

On Tue, Sep 15, 2015 at 5:29 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>1. Fixing periodicity effects on trajectory file (Homa rooz)
>2. Re: Fixing periodicity effects on trajectory file (Justin Lemkul)
>3. Accelerating data analysis. (Dawid das)
>4. Re: Accelerating data analysis. (Justin Lemkul)
>5. Re: Accelerating data analysis. (Erik Marklund)
>6. Re: Accelerating data analysis. (Dawid das)
>7. Re: Accelerating data analysis. (Dawid das)
>
>
> --
>
> Message: 1
> Date: Tue, 15 Sep 2015 16:09:15 +0430
> From: Homa rooz <ha.roozbah...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Fixing periodicity effects on trajectory file
> Message-ID:
> <
> cacc+7lgc90v1vb-7+rfrvdhz4svk5ry8qqoxtu7wjjh1bsi...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi there
> I'm working with gromacs for ligand-protein interaction simulation. I have
> run MD for docked complex and now there is a problem with trajectory
> visualization by VMD. The ligand has left binding site circulating around
> the protein.
> I tried to fix the problem by making index and extract the first frame from
> the trajectory to use as  reference and also running "-center", "no jump",
> "no pbc", "-fit rot" but the problem still exists. I'm quite confused.
> Should I execute fixing command in the special order?
> Which group is more preferred to be located at the center,Protein or
> system(non-solvent)?
> I would be grateful if you could help me in this matter.
> --
> Homa Ahmadi
> Shahed University
> Faculty of Basic Sciences
> Alternative email> h.ahm...@shahed.ac.ir <h.ahm...@ast.ui.ac.ir>
>
>
> --
>
> Message: 2
> Date: Tue, 15 Sep 2015 07:42:37 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Fixing periodicity effects on trajectory file
> Message-ID: <55f8042d.9060...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/15/15 7:39 AM, Homa rooz wrote:
> > Hi there
> > I'm working with gromacs for ligand-protein interaction simulation. I
> have
> > run MD for docked complex and now there is a problem with trajectory
> > visualization by VMD. The ligand has left binding site circulating around
> > the protein.
> > I tried to fix the problem by making index and extract the first frame
> from
> > the trajectory to use as  reference and also running "-center", "no
> jump",
> > "no pbc", "-fit rot" but the problem still exists. I'm quite confused.
> > Should I execute fixing command in the special order?
> > Which group is more preferred to be located at the center,Protein or
> > system(non-solvent)?
>
> If the system is a simple binary protein:ligand complex in water, trjconv
> -center -pbc mol should do it.  Center on the protein, output whatever is
> meaningful to you.
>
> -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
>
> ==
>
>
> --
>
> Message: 3
> Date: Tue, 15 Sep 2015 13:37

Re: [gmx-users] Fixing periodicity effects on trajectory file

[Michael Shirts]

Maybe the ligand actually is leaving the binding site and moving
around, and that's what your simulation is telling you!  Hard to say
with the posted information.

On Tue, Sep 15, 2015 at 11:24 AM, Homa rooz  wrote:
> Dear Justin
> I have followed your advice but it didn't solve my problem.
> Ligand is still out of binding site.
>
> --
> Homa Ahmadi
> Shahed University
> Faculty of Basic Sciences
> Alternative email> h.ahm...@shahed.ac.ir 
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] Fixing periodicity effects on trajectory file

[Homa rooz]

Hi there
I'm working with gromacs for ligand-protein interaction simulation. I have
run MD for docked complex and now there is a problem with trajectory
visualization by VMD. The ligand has left binding site circulating around
the protein.
I tried to fix the problem by making index and extract the first frame from
the trajectory to use as  reference and also running "-center", "no jump",
"no pbc", "-fit rot" but the problem still exists. I'm quite confused.
Should I execute fixing command in the special order?
Which group is more preferred to be located at the center,Protein or
system(non-solvent)?
I would be grateful if you could help me in this matter.
-- 
Homa Ahmadi
Shahed University
Faculty of Basic Sciences
Alternative email> h.ahm...@shahed.ac.ir 
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Fixing periodicity effects on trajectory file

[Justin Lemkul]

On 9/15/15 7:39 AM, Homa rooz wrote:

Hi there
I'm working with gromacs for ligand-protein interaction simulation. I have
run MD for docked complex and now there is a problem with trajectory
visualization by VMD. The ligand has left binding site circulating around
the protein.
I tried to fix the problem by making index and extract the first frame from
the trajectory to use as  reference and also running "-center", "no jump",
"no pbc", "-fit rot" but the problem still exists. I'm quite confused.
Should I execute fixing command in the special order?
Which group is more preferred to be located at the center,Protein or
system(non-solvent)?


If the system is a simple binary protein:ligand complex in water, trjconv 
-center -pbc mol should do it.  Center on the protein, output whatever is 
meaningful to you.


-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] Fixing periodicity effects on trajectory file

[Homa rooz]

Dear Justin
I have followed your advice but it didn't solve my problem.
​Ligand is still out of binding site.

-- 
Homa Ahmadi
Shahed University
Faculty of Basic Sciences
Alternative email> h.ahm...@shahed.ac.ir 
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Re: [gmx-users] Fixing periodicity effects on trajectory file

[Justin Lemkul]

On 9/15/15 1:24 PM, Homa rooz wrote:

Dear Justin
I have followed your advice but it didn't solve my problem.
​Ligand is still out of binding site.



Can you verify that it actually did start in the binding site?  Was everything 
built correctly?  If so, there's no reason that simply centering on the protein 
while putting the molecules in the box wouldn't work.  This is a single-chain 
protein, right?


-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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Gromacs Users mailing list

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