Dear Mark,<br><br>Now, are the files correct?<br><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 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></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>
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