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<P>Dear David:</P>
<P>What I simulated is sugar system, which has no termini. And, the
corresponding residue topology is [GLCA] (alpha-glucose).</P>
<P> </P>
<P>I also know what you mean, but according to the definition of [GLCA], maybe I
could not make the total charge in the system be zero.</P>
<P>Or, other factors are not being considered? What is
your suggestion to this case?</P>
<P> </P>
<P>Thanks very much!</P>
<P> </P>
<P>On Sat, 2004-06-05 at 08:13, Yinghong wrote:<BR>><I> Hi, dear
all:<BR></I>><I> <BR></I>><I> I have a system which have non-zero charges,
normally, we need to add<BR></I>><I> counterions (Na or Cl) to neutralize the
whole system.<BR></I>><I> <BR></I>><I> <BR></I>><I>
<BR></I>><I> However, in my system, when I run "grompp", non-integral charges
(e.g.</I>><I> 1.50e+00) are detected, so under this case, my system
<BR></I>><I> <BR></I>><I> could not keep neutral even if corresponding
ions are added.<BR></I>><I> <BR></I>><I> <BR></I><BR>then you have a
topology problem in your protein.<BR><BR>><I> <BR></I>><I> What should I
do with this kind of problem?<BR></I>><I> <BR></I>><I> Thanks a
lot!<BR></I>><I> <BR></I>><I> <BR></I>><I> <BR></I>><I>
Regards<BR></I>><I> <BR></I>><I> Yinghong<BR></I>><I> <BR></I>><I>
Hongkong University<BR></I>><I> <BR></I>><I> <BR></I>><I>
<BR></I>><I>
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