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.
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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