<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">hm...<div>is it possible that there is partial charge because of terminal of zwitterions?</div><div>(NH3+ and COO-)</div><div><br></div><div>When i tried to make system with terminal of just NH3+ and COO-, there was no partial charge like 5.00.</div><div><br></div><div>But when i used zwitterion terminal, that made the 5.05 charge of the system..</div><div><br></div><div>it can be happened? Or something weird?</div><div><br></div><div>Hyun</div><div><br></div><div><div><div>2011. 4. 6., 오후 5:00, Erik Marklund 작성:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
mohsen ramezanpour skrev 2011-04-06 09.31:
<blockquote cite="mid:BANLkTikA_tDbejmPsM8V0Soj+Up2ZjS_Og@mail.gmail.com" type="cite"><br>
<br>
<div class="gmail_quote">On Wed, Apr 6, 2011 at 11:53 AM, Erik
Marklund <span dir="ltr"><<a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div bgcolor="#ffffff" text="#000000"> Hi,<br>
<br>
No we don't. You can't have fractions of elementary
particles in your molecules.<br>
<br>
</div>
</blockquote>
<div>Dear Erik<br>
<br>
Yes,You are <a href="http://right.It">right.It</a> is obvious .<br>
But I wanted to simulate a part of my system.for example a
part of my protein!<br>
I was wrong,we can't do that <br>
<br>
</div>
</div>
</blockquote>
I think there are several examples of that in literature, e.g. by
Åqvist and coworkers. But think they use a different approach than
just cutting away part of the protein.<br>
<br>
Erik<br>
<blockquote cite="mid:BANLkTikA_tDbejmPsM8V0Soj+Up2ZjS_Og@mail.gmail.com" type="cite">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div bgcolor="#ffffff" text="#000000"> Erik<br>
<br>
mohsen ramezanpour skrev 2011-04-06 09.13:
<div>
<div class="h5">
<blockquote type="cite">Daer Dr.Mark<br>
<br>
You are right,But all of them(as I know) have integer
charges!<br>
the problem is simullating a system with partial
charges.<br>
We absolutely have such systems.<br>
<br>
<div class="gmail_quote">On Wed, Apr 6, 2011 at 11:22
AM, Mark Abraham <span dir="ltr"><<a moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left:
1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt
0.8ex; padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div> On 6/04/2011 4:45 PM, mohsen ramezanpour
wrote:
<blockquote type="cite">Dear Dr.Justin<br>
<br>
What can we do (how can neutralize system)
if the total charge of our system was not
integer?<br>
I think there is not any solution and we
have to simulate a charged system not a
neutral.<br>
Am I right?<br>
</blockquote>
<br>
</div>
I suspect every tutorial for simulating proteins
in water deals with the need for counter-ions,
and the technique for generating them.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite"> Thanks in advance<br>
<br>
<div class="gmail_quote">On Wed, Apr 6,
2011 at 11:12 AM, mohsen ramezanpour <span dir="ltr"><<a moz-do-not-send="true" href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204,
204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">Dear Dr.Justin<br>
<br>
I had the same problem.<br>
I modified the charges and charge
groupsin the topology of a drug.the
net charge of it is zero(I am sure)<br>
though,when I used pdb2gmx it resulted
a NOTE like the following:<br>
<br>
NOTE:The system has non-zero total
charge: 3.000003e00<br>
I continued simulation and ignored it!<br>
Because:<br>
1- I checked my protein.top and qtot
was 3<br>
2-the net charge of my drug was 0<br>
3-Besides,all charges have 3 digit
precision,How can it have 0.000003
additional charge?!<br>
<br>
What is your point of view?<br>
Thanks in advance for your reply
<div>
<div><br>
<br>
<br>
<div class="gmail_quote">On Wed,
Apr 6, 2011 at 3:40 AM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin:
0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
<div><br>
<br>
김현식 wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204);
margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;"> <br>
<br>
> Date: Tue, 5 Apr
2011 23:43:19 +1000<br>
> From: <a moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
> To: <a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> Subject: Re:
[gmx-users] How to remove
charge of 5e-2 ??<br>
><br>
> On 5/04/2011 11:17
PM, Hyunsik wrote:<br>
> > Dear experts,<br>
> ><br>
> > Hi,<br>
> ><br>
> > When prepare a
system, the system had
+5.5. So I add 5 CL- ion
to neutralize.<br>
> ><br>
> > But as you
know, the Cl charge is -1
and there still is 5e-2.
how can i remove that.<br>
><br>
> Your statements are
inconsistent. If you had
5.5 charge and added five<br>
> chloride ions, you
could not end up with
0.05.<br>
<br>
oh.. I have mistaken.. I
had 5.005 of the system
charge.<br>
So even if added five
choride ions, the system
charge is not zero. there
was 0.005<br>
<br>
that is partial charge??
If like that, topology is
broken or something wrong?
abnormal??<br>
<br>
</blockquote>
<br>
</div>
Maybe, maybe not. Rounding
errors could account for this
difference, especially if your
system is very large. Still,
you should inspect your
topology/topologies for
inconsistencies. If pdb2gmx
created the topology, keep an
eye on the "qtot" column for a
running total of the charge.
If you've made or adjusted
any topologies on your own,
double-check your work. If
everything looks correct, then
the difference is likely a
consequence of floating-point
math and nothing more.<br>
<br>
-Justin
<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204);
margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
Thank you,<br>
<br>
Hyun<br>
<br>
><br>
> Mark<br>
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========================================<br>
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Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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<pre cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a moz-do-not-send="true" href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a>
</pre>
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<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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