[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
> <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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

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

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

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