<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Please disregard my previous email. I made a minor mistake when I built the .top file.</span></div><div><br><span></span></div><div><span>Thanks,</span></div><div><br><span></span></div><div><span>Yao<br></span></div><div><br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">From:</span></b> Yao Yao <yao0o@ymail.com><br> <b><span style="font-weight: bold;">To:</span></b> "gmx-users@gromacs.org" <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, February 11, 2012 11:06 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] co-solvent
simulation<br> </font> </div> <br>
<div id="yiv167608150"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;"><div><span>Actually even I follow the "</span><a rel="nofollow" class="yiv167608150moz-txt-link-rfc2396E" target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents">"http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"</a>and try the built-in urea<span> as co-solvent, <br></span></div><div><span>it has the same problem </span><span>(solvate urea as protein can work, but does not work if you consider it as co-solvent).</span></div><div>I do not know if anyone has met the same problem before.</div><div><br></div><div>Thanks,</div><div><br></div><div>Yao<br><span></span></div><div><span><br></span></div><div><br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"> <div dir="ltr">
<font face="Arial" size="2"> ----- Forwarded Message -----<br> <b><span style="font-weight: bold;">From:</span></b> Yao Yao <yao0o@ymail.com><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, February 11, 2012 10:47 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] co-solvent simulation<br> </font> </div> <br>
<div id="yiv167608150"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;"><div><span>Hi Mark,</span></div><div><br><span></span></div><div><span>Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, <br></span></div><div><span>like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"?</span></div><div><br><span></span></div><div><span>Thanks,</span></div><div><br><span></span></div><div><span>Yao<br></span></div><div><br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham
<Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, February 11, 2012 9:39 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] co-solvent simulation<br> </font> </div> <br>
<div id="yiv167608150">
<div>
On 12/02/2012 4:16 PM, Yao Yao wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;">
<div>I am simulating a protein in glycerol solution in amber03
ff and followed
<a rel="nofollow" class="yiv167608150moz-txt-link-rfc2396E" target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents">"http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"</a>.</div>
<div>Since glycerol is not available in amber03.ff by default, I
built it in the ffbonded.itp</div>
</div>
</blockquote>
<br>
You should not need to touch this file to model glycerol. There are
no atom or interaction types that are materially different from
those on peptide side chains.<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;">
<div> and aminoacids.rtp.</div>
<div>For test purpose, I then made a itp for it and solvate it
as a protein and changed .top file accordingly, everything
seems fine when I grompp,</div>
<div>but when I insert it as a co-solvent, it shows like that I
never did claim any bond angles, dihedrals, .... even when I
#include its .itp and change #mols in my new topology.<br>
</div>
</div>
</blockquote>
<br>
You need to work out what is different in the two cases. The diff
tool can be useful here. There is no fundamental difference in the
.top construction for the two cases you are considering - only in
construction of the initial coordinates.<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;">
<div><br>
</div>
<div>I guess the problem is if I do not claim the co-solvent as
a protein, ff will not go to ffbonded.itp to recognize the new
interactions.</div>
<div>Is there any other file for co-solvent interactions I need
to change?</div>
</div>
</blockquote>
<br>
The ffbonded.itp file is #included regardless of what you name your
moleculetypes. You may not be #including the correct one - but then
again I think you should only have the standard one in the first
place.<br>
<br>
Mark<br>
</div>
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