<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 16/03/2012 6:39 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopwcX-0kCxumrfcHdqNC09P=8E6Y0vgCE7GwGmzpaBGCBw@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im">
<blockquote type="cite"> 2) Also I've found that there is
more simple way to define restraines based on the BONDS
enty in the topology file. Could you provide me with the
more information about this simpler way ?<br>
</blockquote>
<br>
</div>
Simpler, but not a restraint to within a region. The manual
section we are discussing links you to the available
documentation elsewhere in the manual. I don't have the time
to help with every interpretation question you might have.<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div class="h5"><br>
</div>
</div>
</div>
</blockquote>
<div>Mark,<br>
<br>
<br>
In more details I want to generate network of disres for all
helices H-bonds. So I want to restraint H-bond distance
between i and i+4 atoms of the backbone.<br>
<br>
What is the simplest way to do such task? I think that the
ussage of genrestr -disre could be useful for such generation
of the complex disres because of the size of my protein. But
how I could define the restrained atoms (i, i+4 atoms ) ? In
the make_ndx options I didnt find the most trivial sollution
of the such choise. So the only sollution is to define each I
and I+4 atoms of the backbone manualy, isnt it ? <br>
</div>
</div>
</blockquote>
<br>
Solving that will require some scripting. Because you know from
genrestr -h that a half a matrix of distance restraints are
generated for the index group chosen, and you only want i->i+4
restraints, you'll need a separate index group for every i->i+4
pair. So you can write a script that loops over calls to make_ndx to
create a group of 2 atoms that are a suitable atom from i and i+4.
Making make_ndx non-interactive (to call it from a script) is
described on the website. Making a shell script to do that is a
skill you will need to learn elsewhere.<br>
<br>
Mark<br>
</body>
</html>