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On 29/03/2012 5:53 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopxhBesTO4D2TmKLPMEO-nAC20QcNT5u6yqDqopsTEMNgg@mail.gmail.com"
type="cite">Mark,<br>
<br>
<br>
thanks for explanation again.<br>
<br>
<br>
<div class="gmail_quote">28 марта 2012 г. 16:04 пользователь 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>
написал: <br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> That can mean big
restraint forces and tiny integration steps and lots of
tweaking and praying. <br>
</div>
</blockquote>
<div><br>
Yes I think this aproach could be usefull in my case. Actually
I want to move some parts of the helices of my protein in the
deired direction up to 6-10 A. There is the data showing that
this new conformation is very unstabile and short-lived in the
absense of some additional external factors. But also I've
seen that application of big restrained forces perturbed the
overal structure of my protein considerably. So the good
sollution might be application of such forces with the
position restraines simultaneously. What do you think about
the most trivial aproach: e.g if I could not applied posres on
the desired atoms and use default posres generated by pdb2gmx
on the all atoms. At the same time I'm using more strongest
distance restrains on the desired positions to move this atoms
even the precense of weaker posres applied on this. Finally
because posres act on the others atoms I can prevent
destabilisation of the whole protein. Might this aproach be
usefull? And what difference between forses of the posres (
1000 kj) and disres must be to generate expected effect ?<br>
</div>
</div>
</blockquote>
<br>
Yeah, some kind of hybrid treatment of distance and position
restraints could be required. I've no idea on required force
constants - this kind of thing (breaking the force field to set up
initial conditions that you expect are fairly unphysical) is very
situation dependent. Nobody really does it often enough for there to
be a general body of knowledge.<br>
<br>
Mark<br>
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