Dear colleagues, I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using "position restraints" for few of those residues as well as to the two ends of one of the subunits, in which there are missing residues.
[ position_restraints ] ; atom type fx fy fz 457 1 1000 1000 1000 459 1 1000 1000 1000 460 1 1000 1000 1000 461 1 1000 1000 1000 After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. 1) Is this because of imposing position restraints or is it because of the gap between two subunits in on the subunits? 2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? Coming to the missing residues part, I decided to use distance restraints between the two ends. Please note that only one of the chain is in covalently linked with the transmembrane domain. Rest of them have vanderwaals interactions. Thanks for any kind of suggestion in this regard. Prema.
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