From: Benjamin D Madej <>
Date: Thu, 12 Jun 2014 18:27:54 +0000


Yes, it is a bit strange that the charges do not add up to zero. Any combination of Lipid14 charges should sum to zero charge. Meaning, any combination of PC, PE, LA, MY, PA, OL should sum to 0.0. What type of lipids are you using again and how many?

Also, I would verify that LEaP is correctly recognizing all of the residues in your system and correctly assigning atom types and charges. I would check the warnings and errors again for any problems.

The issue might be in the protein portion of your system as well. For example, are the amino acids correctly assigned? These are the things that I would examine before going further with ionization and MD simulation.

All the best,
Ben Madej
UCSD Chemistry and Biochemistry
From: James Starlight []
Sent: Wednesday, June 11, 2014 10:45 PM
To: AMBER Mailing List
Subject: Re: [AMBER]


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
> _______________________________________________
> AMBER mailing list
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Received on Thu Jun 12 2014 - 12:00:06 PDT
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