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

[Mark Abraham]

On 24/02/2012 6:55 PM, James Starlight wrote:
> Mark,
>
> what about the next sollution
>
> firstly I'll align both of my structures ( x-ray with water and 
> another my model without water)
>
> than I'll copy aligned water from first structure to my model in the 
> bottom of the GRO file.
>
> than I'll minimise this editted structure to relax side chains of the 
> residues wich are in contact with the new waters
>
> Might this aproach be usefull? Commonly I use it to prepare 
> protein-ligand complexes.

Might work, but there are lots of steric issues and potential problems.

Mark

>
> James
>
> 2012/2/24 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     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.
>
>     Mark
>
>
>>
>>     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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