[gmx-users] Internal water in the membrane receptor

James Starlight 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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