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On 27/01/2011 7:23 PM, Chih-Ying Lin wrote:
<blockquote
cite="mid:AANLkTikx6rZPgB=Yrq4wBVByEmVVusGHE6r3adU3W3_f@mail.gmail.com"
type="cite">
<div><span class="Apple-style-span" style="font-family:
arial,sans-serif; font-size: 13px; border-collapse: collapse;"><br>
Hi<br>
I issued "pdb2gmx with G45a3 force field" on the "bovine
carbonic anhydrase" <br>
<br>
<br>
From the .top value, the ZN+2 is given qtot 1.233e-06 ......<br>
<br>
<br>
<br>
2611 ZN2+ 257 ZN ZN 1137 2
65.37 ; qtot 1.233e-06<br>
<br>
<br>
I am confused with the charges.<br>
Isn't ZN+2 carrying +2 charges ??<br>
<br>
<br>
</span></div>
<div><span class="Apple-style-span" style="font-family:
arial,sans-serif; font-size: 13px; border-collapse: collapse;">From
Mark =><br>
It is - look at the column headings higher up. See <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic"
target="_blank" style="color: rgb(0, 0, 204);">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a>for
why the total charge doesn't look nice.<br>
<br>
<br>
</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">However,</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><span
class="Apple-style-span" style="font-size: 13px;">qtot
1.233e-06 ~ 0 isn't it away from +2 charges too much?</span></span></font></div>
</blockquote>
<br>
qtot is not the atomic partial charge. Like I said last time "<span
class="Apple-style-span" style="font-family: arial,sans-serif;
font-size: 13px; border-collapse: collapse;">look at the column
headings higher up"<br>
<br>
Mark<br>
</span><br>
<blockquote
cite="mid:AANLkTikx6rZPgB=Yrq4wBVByEmVVusGHE6r3adU3W3_f@mail.gmail.com"
type="cite">
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">Or,
it is the tolerable ?</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">Thank
you</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;">Lin</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span
class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div>
</blockquote>
<br>
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