<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'><P>Dear Gromacs USERs,</P>
<P>My ligand, which contains a piperazine ring & needs to be positively charged (+1). </P>
<P>When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen. </P>
<P>But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733 on this atom. So does it mean it has put partial charge as (F.Charge - P. Charge). When I use InsightII (cff91 FF), the partial charge on this ligand was -0.556 and also it had a formal charge of +1. So kindly suggest me the best way out.</P>
<P> </P>
<P>Also, does gromacs takes formal charges automatically or is there a way to define the same. </P>
<P> </P>
<P>thanks</P>
<P>nahren</P><FONT face=Arial size=2></FONT></td></tr></table><br>