<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Thanks <font size="2" face="Arial">Francesco.</font></span></div><div><span><font size="2" face="Arial"></font></span> </div><div><span><font size="2" face="Arial">But at any pH value (different protonation state), the H cannot be regarded as fully associated or dissociated. Thus can we further consider whether the total charge calculated by pdb2gmx is really the net charge of the system or not. I regard the net total charge, regardless of positive or negative, can hardly be an integer.</font></span></div><div><span><font size="2" face="Arial"></font></span> </div><div><span><font size="2" face="Arial">Furthermore, if we do not add couter ions to make the net charge "0" for the whole system and we do the MD, what can occur?</font></span></div><div><span><font size="2"
face="Arial"></font></span> </div><div><span><font size="2" face="Arial">Cheers,</font></span></div><div><span><font size="2" face="Arial"></font></span> </div><div><span><font size="2" face="Arial">Acoot</font></div></span><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 size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight: bold;">From:</span></b> Francesco Oteri <francesco.oteri@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, 7 April 2012 7:14 PM<br> <b><span style="font-weight:
bold;">Subject:</span></b> Re: [gmx-users] how pdb2gmx calculate the total charge of a protein<br> </font> </div> <br><meta content="off" http-equiv="x-dns-prefetch-control"><div id="yiv282247265">
<div>
Dear Acoot,<br>
the error, I guess, is you assumed the histidines are positive while
I think they are neutral.<br>
Since the His protonation state is hard to identify at ph7,
Hystidines are usually neutral.<br>
<br>
Francesco<br>
<br>
<br>
Il 07/04/2012 09:42, Acoot Brett ha scritto:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<div><br>
Dear All,</div>
<div> </div>
<div>I have a protein, the charged residue numbers in the
protein is as following</div>
<div>ARG 11<br>
ASP 19<br>
glu 25<br>
his 8<br>
lys 24</div>
<div> </div>
<div>asp+glu= 44<br>
arg+his+lys=43</div>
<div> </div>
<div>However the total charge of the protein given by pdb2gmx is
-9.</div>
<div> </div>
<div>Will you please introduce to me how pdb2gmx calculate the
total charge of the protein?</div>
<div> </div>
<div>Cheers,</div>
<div> </div>
<div>Acoot</div>
</div>
<br>
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<br>
</blockquote>
<br>
</div>
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