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>
Any suggestions are appreciated!<br><br>Yours<br>Xin<br>