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 <[email protected]
<mailto:[email protected]>>
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 <[email protected]
<mailto:[email protected]>>
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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