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On 24/02/2012 6:55 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzgE7w17y7Tq4M7gdFCHkr+kYWCeHrGv3qtMXUNAxEYRQ@mail.gmail.com"
type="cite">Mark,<br>
<br>
what about the next sollution<br>
<br>
firstly I'll align both of my structures ( x-ray with water and
another my model without water) <br>
<br>
than I'll copy aligned water from first structure to my model in
the bottom of the GRO file.<br>
<br>
than I'll minimise this editted structure to relax side chains of
the residues wich are in contact with the new waters<br>
<br>
Might this aproach be usefull? Commonly I use it to prepare
protein-ligand complexes.<br>
</blockquote>
<br>
Might work, but there are lots of steric issues and potential
problems.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzgE7w17y7Tq4M7gdFCHkr+kYWCeHrGv3qtMXUNAxEYRQ@mail.gmail.com"
type="cite">
<br>
James<br>
<br>
<div class="gmail_quote">2012/2/24 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div class="im"> On 24/02/2012 6:31 PM, James Starlight
wrote:
<blockquote type="cite">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>
</blockquote>
<br>
</div>
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.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark</font></span>
<div class="im"><br>
<br>
<blockquote type="cite"> <br>
James<br>
<br>
<div class="gmail_quote">2012/2/22 James Starlight <span
dir="ltr"><<a moz-do-not-send="true"
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>
</font></span></blockquote>
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