Thanks Mark, I will try that out :)<br><br>
<div class="gmail_quote">On Mon, May 5, 2008 at 12:01 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>
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<div class="Wj3C7c">xin liu wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear GMX-Users<br><br>I want to perform a MDS with lignd solvted in DMSO, this is how I setup the top file:<br>
<br>#include "ffgmx.itp"<br>#include "lig_ffgmx.itp"<br>#include "dmso.itp"<br><br>[ molecules ]<br>; name number<br>Protein 1<br>DMSO 3245<br><br>My system works fine with "ffgmx.itp". However, after I changed the parameters to "ffG43a1.itp" and "lig_ff43a1.itp" accordingly, the grompp command complains about "Atomtype 'SD' not found". I think this probably because the program didn't recognize the DMSO atomtype, but how should I setup the top file so as to include it properly and avoid the error? I think I might have missed some fundamental clues when seting up the FF43a1 top file.<br>
</blockquote><br></div></div>Yep. The fundamental principle is not to mix force fields. Absent a cunning construction of your dmso.itp, it will be for working with one force field only. If you wish to change force fields (and you should, because use of ffgmx is deprecated) then you need to find a DMSO model suitable for use with that other force field. Hopefully there will already exist a suitable dmso.itp file, but likely you'll have to create such a file yourself from the parameters given. This will require a sound knowledge of chapter 5 of the GROMACS manual. Also check out <a href="http://wiki.gromacs.org/index.php/Force_Fields" target="_blank">http://wiki.gromacs.org/index.php/Force_Fields</a> and <a href="http://wiki.gromacs.org/index.php/Parameterization" target="_blank">http://wiki.gromacs.org/index.php/Parameterization</a><br>
<br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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