Hi, Justin: <br>I am reading chapter 5 now. Still feel confused. I wrote methane.top file like this: <br><br>; Methane topology file<br>;<br>; The force field files to be included<br>#include "ffoplsaa.itp"<br><br>
[ moleculetype ]<br>; Name nrexcl<br> METH 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 opls_138 1 METH C 1 -0.24 12.011 ; qtot 0.61<br>
2 opls_140 1 METH H 1 0.06 1.008 ; qtot 0.67<br> 3 opls_140 1 METH H 1 0.06 1.008 ; qtot 0.67<br> 4 opls_140 1 METH H 1 0.06 1.008 ; qtot 0.73<br>
5 opls_140 1 METH H 1 0.06 1.008 ; qtot 0.79<br><br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br> 1 2 1<br> 1 3 1<br>
1 4 1<br> 1 5 1<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>; Include water topology<br>#include "spc.itp"<br><br>[ system ]<br>
; Name<br>Methane<br><br>[ molecules ]<br>; Compound #mols<br>METH 1<br>; ;;;;;;;<br><br>Then I should go to ffoplsaa.rtp file to add a new molecule like : <br><br>[METH]<br> [ atoms ]<br> C opls_135 -0.240 1<br>
HC1 opls_140 0.060 1<br> HC2 opls_140 0.060 1<br> HC3 opls_140 0.060 1<br> HC4 opls_140 0.60 1<br> [ bonds ]<br> C HC1<br> C HC2<br> C HC3<br> C HC4<br>
;;;;;;;<br><br>Is that reasonable? Thanks for your help.<br><br><br><div class="gmail_quote">On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul <span dir="ltr"><<a 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>
xianghong qi wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field?<br>
Thanks in advance.<br>
<br>
</blockquote>
<br></div>
For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>
-Xianghong Qi<br>
<br>
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Virginia Tech<br>
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