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 <jmsstarli...@gmail.com
<mailto:jmsstarli...@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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
