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On 5/04/2011 9:59 PM, ahmet yżldżrżm wrote:
<blockquote
cite="mid:BANLkTi=FZcNJYKMBFfu8=QYpRSD9Ux_LxQ@mail.gmail.com"
type="cite">Dear Mark,<br>
<br>
Now, are the files correct?<br>
</blockquote>
<br>
They're well-formed, but you've not taken Tsjerk's advice and
arranged for (COH)3(NH3+)C to have charges consistent with its
symmetry. When people donate their time to you, please use it or
demonstrate why you shouldn't :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=FZcNJYKMBFfu8=QYpRSD9Ux_LxQ@mail.gmail.com"
type="cite"><b>EDO.itp</b>:<br>
[ moleculetype ]<br>
; Name nrexcl<br>
EDO 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 OA 1 EDO OAB 1 -0.111 15.9994 <br>
2 H 1 EDO HAE 1 0.031 1.0080 <br>
3 CH2 1 EDO CAA 1 0.080 14.0270 <br>
4 CH2 1 EDO CAC <b>2</b> 0.080
14.0270 <br>
5 OA 1 EDO OAD <b>2</b> -0.111
15.9994 <br>
6 H 1 EDO HAF <b>2 </b> 0.031
1.0080 <br>
<br>
<b>TRS.itp:</b><br>
[ moleculetype ]<br>
; Name nrexcl<br>
TRS 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 OA 1 TRS O1 1 -0.119 15.9994 <br>
2 H 1 TRS H13 1 0.032 1.0080 <br>
3 CH2 1 TRS C1 1 0.087 14.0270 <br>
4 CCl4 1 TRS C <b>3</b> 0.055
12.0110 <br>
5 CH2 1 TRS C3 <b> 4 </b> 0.049
14.0270 <br>
6 OA 1 TRS O3 <b>4</b> -0.205
15.9994 <br>
7 H 1 TRS H33 <b> 4</b> 0.019
1.0080 <br>
8 NL 1 TRS N <b> 5</b> 0.206
14.0067 <br>
9 H 1 TRS H2 <b> 5</b> 0.004
1.0080 <br>
10 H 1 TRS H3 <b>5</b> 0.004
1.0080 <br>
11 H 1 TRS H1 <b>5 </b> 0.004
1.0080 <br>
12 CH2 1 TRS C2 <b>6 </b> 0.150
14.0270 <br>
13 OA 1 TRS O2 <b>6</b> -0.205
15.9994 <br>
14 H 1 TRS H23 <b> 6</b> 0.019
1.0080 <br>
<br>
Thanks for your helps<br>
<br>
<div class="gmail_quote">05 Nisan 2011 09:03 tarihinde 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>
yazdż:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div>
<div> On 5/04/2011 3:57 PM, ahmet yżldżrżm wrote:
<blockquote type="cite">Dear Tsjerk,<br>
<br>
<blockquote style="margin: 0pt 0pt 0pt 0.8ex;
border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;" class="gmail_quote">Hi Ahmet,<br>
<br>
As suggested, it's better to break up your molecule
into smaller<br>
charge groups. Note that charge groups don't need to
have zero charge,<br>
nor integer charge. In your case, I'd suggest two
COH groups for EDO,<br>
which will have zero net charge each, and for TRS
I'd take the COH<br>
groups as separate charge groups. I also note that
the COH groups,<br>
although chemically identical - H3NC(COH)3, right?-,
have different<br>
charges. That doesn't seem proper.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
</blockquote>
<br>
nonrevised .itp file:<br>
EDO 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge
mass<br>
1 OA 1 EDO OAB 1 -0.111
15.9994 <br>
2 H 1 EDO HAE 1 0.031
1.0080 <br>
3 CH2 1 EDO CAA 1 0.080
14.0270 <br>
4 CH2 1 EDO CAC 1 0.080
14.0270 <br>
5 OA 1 EDO OAD 1 -0.111
15.9994 <br>
6 H 1 EDO HAF 1 0.031
1.0080 <br>
<br>
nonrevised .itp file:<br>
EDO 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge
mass<br>
1 OA 1 EDO OAB 1 -0.111
15.9994 <br>
2 H 1 EDO HAE 1 0.031
1.0080 <br>
3 CH2 1 EDO CAA 1 <b>0.000</b>
14.0270 <br>
4 CH2 1 EDO CAC 1 <b>0.000</b>
14.0270 <br>
5 OA 1 EDO OAD 1 -0.111
15.9994 <br>
6 H 1 EDO HAF 1 0.031
1.0080 <br>
<br>
can you show me on the itp file? how do I seperate two
COH groups? Please help me<br>
</blockquote>
<br>
</div>
</div>
We didn't say to use zero *charges*. We said you need small
charge groups. Since EDO is neutral, then by symmetry each
half must also be neutral.<br>
<br>
Have a look at the way charge groups are used in the .rtp
file for your forcefield. You need to do similar things. If
you don't understand the file formats yet, you need to read
up on chapter 5 of the manual.<br>
<br>
Mark<br>
</div>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
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