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On 9/01/2012 4:53 PM, John Ladasky wrote:
<blockquote
cite="mid:1326088429.2814.YahooMailNeo@web120603.mail.ne1.yahoo.com"
type="cite">
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<div style="font-family: arial, helvetica, sans-serif;
font-size: 10pt; "><span>Hello everyone,</span></div>
<div style="font-family: arial, helvetica, sans-serif;
font-size: 10pt; "><span><br>
</span></div>
<div style="font-family: arial, helvetica, sans-serif;
font-size: 10pt; "><span>I've used the rot+trans option in
GROMACS trjconv to superimpose groups of atoms within a
single molecular dynamics simulation. I am now interested
in modeling a protein, and a rather thoroughly scrambled
circular permutation of that same protein. I want to
construct a superimposition which optimizes the alignment of
selected residues within the two structures. But unlike in
a standard trjconv superimposition, I will be trying to
align atoms in one structure which correspond to atoms with
different numbers in the other structure. So the idea of
groups as numbered atoms, as conventionally defined in a
GROMACS .ndx file, would not seem to apply here.</span></div>
<div style="font-family: arial, helvetica, sans-serif;
font-size: 10pt; "><span><br>
</span></div>
<div style="font-family: arial, helvetica, sans-serif;
font-size: 10pt; "><span>Is this a practical task within
GROMACS, or should I be looking elsewhere for the tool to
accomplish the job?</span></div>
<br>
</div>
</blockquote>
<br>
Doesn't trjconv -fit rot+trans prompt for a group for each structure
for the superposition? If so, you should be able to construct an
index file with groups like<br>
<br>
[ normal ]<br>
<br>
3 45 223<br>
<br>
[ scrambled ]<br>
<br>
451 97 345<br>
<br>
and fit those.<br>
<br>
Mark<br>
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