Re: [gmx-users] Simulation of membrane associated protein

[Olga Press]

Thank you!

*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel
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Re: [gmx-users] Simulation of membrane associated protein

[Justin Lemkul]

On 10/4/19 4:52 AM, Olga Press wrote:

Prof. Lemkul thank you for your response.
I'm using the output file from the charmm gui site after the MD production,
which contain an equilibrated DOPC bilayer with TIP3 molecules  as the
solvent (and I remove the ions before the solvation).
I used the second option of the gmx_solvate (solvate a solute configuration)
Do you suggest to remove the water molecule, than concatenate the protein
coordinates with the lipids coordinates and than solvate it with water?


Yes, otherwise reposition the protein so it is further away from the 
membrane and does not lead to lipid deletion.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Simulation of membrane associated protein

[Olga Press]

Prof. Lemkul thank you for your response.
I'm using the output file from the charmm gui site after the MD production,
which contain an equilibrated DOPC bilayer with TIP3 molecules  as the
solvent (and I remove the ions before the solvation).
I used the second option of the gmx_solvate (solvate a solute configuration)
Do you suggest to remove the water molecule, than concatenate the protein
coordinates with the lipids coordinates and than solvate it with water?
Thank you.


‫בתאריך יום ה׳, 3 באוק׳ 2019 ב-22:46 מאת ‪Justin Lemkul‬‏ <‪jalem...@vt.edu
‬‏>:‬

>
>
> On 10/2/19 10:58 AM, Olga Press wrote:
> > Dear all,
> > I am working on DOPC-associated protein and try to orient the protein on
> > the DOPC surface by using the gmx_solvate as previously suggested by
> Prof.
> > Justin Lemkul at the following like
> > http://www.mdtutorials.com/gmx/biphasic/03_tricks.html
> > <
> https://www.researchgate.net/deref/http%3A%2F%2Fwww.mdtutorials.com%2Fgmx%2Fbiphasic%2F03_tricks.html
> >
> > .
> > The protein reaches the desired position, however together with the TIP3
> > molecules, there is a removal of several lipids, although there was no
> > overlap between the protein and the lipids. (instead of 260 lipids I get
> > 243 lipids)
> > What can I do to prevent removal of lipids? any suggestions?
>
> What are you doing that causes removal of lipids? If you're
> concatenating protein coordinates with lipid coordinates, then solvating
> with water, there should be no way for lipids to be removed. If lipids
> are removed because you are using them as a "solvent" for the protein,
> that just means the placement of the protein is not correct.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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> Gromacs Users mailing list
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> posting!
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>


-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel
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Re: [gmx-users] Simulation of membrane associated protein

[Justin Lemkul]

On 10/2/19 10:58 AM, Olga Press wrote:

Dear all,
I am working on DOPC-associated protein and try to orient the protein on
the DOPC surface by using the gmx_solvate as previously suggested by Prof.
Justin Lemkul at the following like
http://www.mdtutorials.com/gmx/biphasic/03_tricks.html

.
The protein reaches the desired position, however together with the TIP3
molecules, there is a removal of several lipids, although there was no
overlap between the protein and the lipids. (instead of 260 lipids I get
243 lipids)
What can I do to prevent removal of lipids? any suggestions?


What are you doing that causes removal of lipids? If you're 
concatenating protein coordinates with lipid coordinates, then solvating 
with water, there should be no way for lipids to be removed. If lipids 
are removed because you are using them as a "solvent" for the protein, 
that just means the placement of the protein is not correct.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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