[gmx-users] Re: Internal water in the membrane receptor

James Starlight jmsstarlight at gmail.com
Fri Feb 24 08:31:44 CET 2012

Up! :)

Please provide me with the best sollution of my problem! I just want to
copy some water mollecules from X-ray structure to my model and place it in
the identical possitions inside the TM budle of my protein.  What are the
most trivial way to solve this task?


2012/2/22 James Starlight <jmsstarlight at gmail.com>

> 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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