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

[James Starlight]

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.

James

2012/2/24 Mark Abraham <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>
>
>> 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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