Hi there<br><br>The amide partial charges in the share folder of gromacs G56A3ff is as following<br> H H: +0.280 N: -0.280<br> | C: -0.380 O: -0.380<br>C-N-C-C other C : 0.000<br>
"<br> O<br><br>I guess all protein people use partial charges of amide like above because it is in the forcefield file? I am wondering where are those numbers come from? Any reference will be great! <br>
(I know in Justin Lemkul 2010 paper he discusses about the partial charges of amide. I am curious about how gromacs sign those numbers. It must be good although different form gaussian calculations.)<br><br>Thank you for your time!<br>
<br>Cheers!<br>Xueming<br>