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

[James Starlight]

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?

James

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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