[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 <‪jalemkul at 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
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel