[gmx-users] Pulling protein from distance on membrane

[Justin Lemkul]

On 2/13/18 5:24 AM, Souparno Adhikary wrote:
> Hi,
>
> I am trying to simulate a system in which a protein will be pulled from a
> distance and ultimately be put on a DPPC membrane system. I went through
> Lemkul's tutorial on membrane and successfully simulated protein-membrane
> systems before.
>
> In this case, I put the protein in the required coordinates using editconf
> (distant from the membrane). Whenever I'm running the inflategro script
> (provided by Justin Lemkul in his webpage), the system breaks apart
> (specifically the protein).
>
> Please give me an idea how can I put the protein outside the membrane and
> then pull it on the membrane.

If the protein is outside the membrane, why are you running InflateGRO? 
That's only for packing lipids around an embedded membrane.

Define a proper box, position the components in it, solvate and add 
ions, and proceed. There's no need for extra work.

-Justin

> To say about the protein, it is not usually considered a membrane
> interacting protein. Some recent publications highlighted the activity of
> the protein as it pulls away some of the membrane lipids after interacting.
> Earlier, when I've simulated the protein in the membrane and put some weak
> force on the protein to make it go away from the membrane, I have
> successfully found the experimental results. Now, I want to put the protein
> from outside the membrane (as the phenomenon takes place in the in vitro
> system).
>
> Thanks in advance,
>
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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