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On 13/03/2012 1:13 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopy9xW_T3_ys2Kr_JpaKPmV77Fxw1aOQ=-L-o0XVgTyWZg@mail.gmail.com"
type="cite">Francesca,<br>
<br>
Yes I suppose this is good aproach for the generation of position
restricktions on the desired atoms. But I want to restrain the
distance between selected pairs of atoms ( e.g between C-alpha-
C-alpha atoms of two different residues).<br>
</blockquote>
<br>
The help for genrestr -disre says that this is exactly what it
does... use an index group to make distance restraints.<br>
<br>
<blockquote
cite="mid:CAALQopy9xW_T3_ys2Kr_JpaKPmV77Fxw1aOQ=-L-o0XVgTyWZg@mail.gmail.com"
type="cite">
<br>
Also I want to restrain some dihedral angles in the desired
rotameric forms.<br>
<br>
In literature I've found that peple have dome the same things in
Gromacs but I could not find detailed algorithm of such
methodology :(<br>
</blockquote>
<br>
There can't be a walk-through of everything anybody might ever do,
unfortunately. Manual chapter 4 talks about the functional forms
available. There's a table in section 5.5 that describes how to
construct the line of a [ moleculetype ] section. That's all you
need to know if have a general understanding of how the .top file
works (elsewhere in chapter 5).<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopy9xW_T3_ys2Kr_JpaKPmV77Fxw1aOQ=-L-o0XVgTyWZg@mail.gmail.com"
type="cite">
<br>
James<br>
<br>
<div class="gmail_quote">12 марта 2012 г. 18:05 пользователь
francesca vitalini <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:francesca.vitalini11@gmail.com">francesca.vitalini11@gmail.com</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I
think you can make an index file using make_ndx where you
specify<br>
the atoms you want to restraint.<br>
Hope this can help.<br>
Francesca<br>
<br>
2012/3/12 James Starlight <<a moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>>:<br>
<div class="HOEnZb">
<div class="h5">> Dear Gromacs users!<br>
><br>
><br>
> I want to perform constrained MD simulation of my
protein with inclusion of<br>
> some experimental restraints.<br>
><br>
><br>
> 1) I found that genrest cpmmand could be usefull for
the generation of the<br>
> distance restrictions wich I could use in my
constrined simulation.<br>
><br>
> Also in manual I've found that command like<br>
><br>
> genrestr -f b2ar.gro -disre -index.ndx -o test.itp<br>
><br>
> will produce some distance restricted matrix of the
whole groups presented<br>
> in the index.ndx file.<br>
><br>
> So how I could select to contrain selected residues
within selected distance<br>
> by means the index file? E.g I've manually point out
2 residues in<br>
> index.ndx. I waant to preserve between that residues
some desired distance D<br>
> wich I've obtaine from the experimental data. How I
could do it via genrestr<br>
> and waht addition flags should I use for that purpose
?<br>
><br>
><br>
> 2) Is there any way to apply gradually the desired
dist.resrs during MDrun<br>
> to prevent some artifacts in my system wich would
occur due to the rapid<br>
> application of the dis.res ( e.g in cases where the
conformation of the<br>
> started structure and that wich I'd obtained fter
application of the<br>
> restrains are slightly different)?<br>
><br>
> Thanks for help,<br>
><br>
><br>
> James<br>
><br>
</div>
</div>
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