Up! :)<br><br>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?<br>
<br>James<br><br><div class="gmail_quote">2012/2/22 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users!<br><br>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.<br>
<br><br>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).<br>
<br>So what the best way to build system would be in my case?<br><br>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 ?<br>
<br>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 ? )<br><br>Thanks for help<span><font color="#888888"><br>
<br><br>James<br>
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