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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 24 08:36:21 CET 2012

On 24/02/2012 6:31 PM, James Starlight wrote:
> 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?

You have a non-trivial problem. You can either build the model on the 
structure that has the waters (pdb2gmx doesn't strip water, IIRC), or 
work out some geometric criteria for placing the waters afterwards. Not 
every problem has an existing tool for its solution.


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