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On 16/06/2012 5:03 PM, delara aghaie wrote:
<blockquote
cite="mid:1339830224.20467.YahooMailNeo@web28702.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;">
<div><span>Dear Mark</span></div>
<div><span>Many thanks for your response.</span></div>
<div><br>
<span></span></div>
<div><span>Now A question: <br>
</span></div>
<div><span>I have read multiple chains section in gromacs
website. It says take a structure file with single chain and
use pdb2gmx on it. In the resulting .top file at the end of
file, we see</span></div>
<div><span>{molecule}</span></div>
<div><span>protein</span></div>
<div><span>we should change the protein number to the number of
identical chains. and then submit this .top with the
coordinate file containing the same number of chains as
mentioned in .top file: (((I have the pdf format of
structure for 2 chains, How can I get the .gro file for
them?</span></div>
</div>
</blockquote>
<br>
You don't need a .gro file: <a
href="http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#section_1">http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#section_1</a>.
You need a coordinate file that matches the contents of the .top
file. Whether that is easy depends what you did with pdb2gmx.<br>
<br>
<blockquote
cite="mid:1339830224.20467.YahooMailNeo@web28702.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;">
<div><span> as I have done pdb2gmax on a single chain, I do not
have a .gro file containing 2 chains. Should I separately do
pdb2gmax on this .top file to get .gro containing 2
chains?))))</span></div>
<div><br>
<span></span></div>
<div>--------------------</div>
<div>As a test, Once I did pdb2gmx on a source pdb file of 1RFB.
As a result I have .gro file which has putted the aminoacides
of the second chain after the first chain without separating
them. (This does not show the protein as two separate chains
!! ). Also it gives .top files separately for each chain. Are
these results correct??</div>
<div>-------------------------<br>
<span></span></div>
<div><br>
</div>
</div>
</blockquote>
<br>
See pdb2gmx -h for how to do chain management - but if you can run
pdb2gmx on your multi-chain coordinate file, then you don't need to
get involved with the contents of <a
href="http://www.gromacs.org/Documentation/How-tos/Multiple_Chains">http://www.gromacs.org/Documentation/How-tos/Multiple_Chains</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1339830224.20467.YahooMailNeo@web28702.mail.ir2.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:arial,
helvetica, sans-serif;font-size:12pt">
<div><span></span></div>
<div>Regards</div>
<div>D.M<br>
<span></span></div>
<div><br>
<span></span></div>
<div><span>-</span></div>
<div><br>
</div>
<div style="font-family: arial, helvetica, sans-serif;
font-size: 12pt;">
<div style="font-family: times new roman, new york, times,
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<div dir="ltr"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Friday, 15 June 2012, 12:03<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] simulating dimer proteins<br>
</font> </div>
<br>
<div id="yiv1436248926">
<div> On 15/06/2012 3:56 PM, delara aghaie wrote:
<blockquote 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 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>
</div>
</div>
<br>
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