Dear Gromacs Users! I want to perform simulation of the membrane receptor in the membtane environment. There are some evidence about precense of the functional-relevant internal water mollecules in the transmembrane alpha-helix bundle of the receptor.
I want to take into account that internal water in my model. I have coordinates of the X-ray structures wich have all that water. Also I have perfect model of the same protein wich have not that water but have full-length structure ( there are some missing residues in the X-ray structures- e.g in the loop regions). So what the best way to build system would be in my case? 1- Should I use X-ray structure where internal water has already present and build missing loops via model software ? How I could preserve the internal waters in that starting structure when this structure will be processed by pdb2gmx ? 2- Or the best way is to incorporate all waters in the model of my protein ? If this aproach could be better what is the simplest way to transfer exact coordinates of water in that holo model ? ) Thanks for help James
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