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On 15/06/2012 3:56 PM, delara aghaie wrote:
<blockquote
cite="mid:1339739774.96024.YahooMailNeo@web28705.mail.ir2.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: arial,helvetica,sans-serif; font-size: 12pt;">Dear
Gromacs users<br>
I want to compare some properties of two Interferons via MD
simulation.<br>
One comes with pdb ID : 1ITF. (It has 24 Models in single pdb
file, but each model with single chain.) I did pdb2gmx on this.<br>
<br>
The other is with pdb ID of : (1RFB). This has two chanis<br>
--------------------------------<br>
DBREF 1RFB A 1 119 UNP P07353 IFNG_BOVIN 24
142<br>
DBREF 1RFB B 1 119 UNP P07353 IFNG_BOVIN 24
142<br>
-------------------------------<br>
<br>
Now the question: Is it wise to select only chain A and do the
simulations on it in order to compare with the 1ITF, which has
one chain?.<br>
I have read about simulating multiple chains in manual. But I
think the comparison between a protein with single chain and the
other with two chains may not be correct. (I want to compare
gyration radiuses and secondary structures)<br>
</div>
</blockquote>
<br>
The number of chains is not really the issue - you want to compare
things that are comparable. If 1RFB contains a dimeric structure
that does the same job as the monomeric 1ITF then they might be
comparable.<br>
<br>
<blockquote
cite="mid:1339739774.96024.YahooMailNeo@web28705.mail.ir2.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:arial,
helvetica, sans-serif;font-size:12pt"> I want to know if it is
common to do MD on selected chain of a dimer?<br>
</div>
</blockquote>
<br>
It happens. Whether it makes scientific sense in your case is
something you have to address.<br>
<br>
Mark<br>
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