From: James Starlight <>
Date: Thu, 12 Jun 2014 09:45:00 +0400


Thanks a lot! It's strange that having the same input I've obtained
difference in total charge with different lipid force fields. It indicates
that problem might be with the lipid not protein mightn't it? In any case
is there any possibility to 0.999040 => 1 for further proper ionization of
my system


2014-06-12 0:47 GMT+04:00 Benjamin D Madej <>:

> James,
> The charge of the unit is 0.999040 which is fairly close to 1.0. This
> warning is useful for checking your units total charge because it may
> indicate missing atoms or incorrect unit topology. Check that all the atoms
> are present and that the bonding is correct in that unit.
> I think it should be fairly easy to search for atoms within a certain
> range of Z coordinates. Probably VMD or PyMOL can do this. Or it could be
> scripted in BASH or Python as well. Once you know which molecules need to
> be deleted, then it's just a matter of writing a script to remove the
> molecules from your input structure file.
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
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Received on Wed Jun 11 2014 - 23:00:02 PDT
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