Re: AMBER: ADDIONS do not neutralize to ZERO

From: Chris Moth <>
Date: Mon, 29 Jan 2007 15:30:20 -0600

It sounds like you have many hundreds of DMP residues and these
non-integral charges are adding up badly.

If this is the case, you may want to take time to use the RED perl
scripts with multiple orientations of DMP - and possibly multiple

This may give you greater confidence in your DMP charges. Then, if you
still must hand-adjust some atoms by .000005 or so, I believe that you
can do this without much guilt.


Adding .00005 charge units to 4 DMP atoms to solve this is

Regarding my charge of 0.970410 in the system, I checked and my system
> without ligand, and you are right>>
> Total unperturbed charge: 13.9705
> Total perturbed charge: 13.9705
> So, my system (protein-lipid-water) essentially has a + 13.9705 charge. Now,
> I also checked my lipid (DMP) unit for charge, and although it should be
> neutral, It has a residual charge of::

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Received on Wed Jan 31 2007 - 06:07:26 PST
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