[gmx-users] Internal water in the membrane receptor
jmsstarlight at gmail.com
Wed Feb 22 14:26:47 CET 2012
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
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