AMBER Archive (2006)

Subject: Re: AMBER: Leap: neutralising the charge

From: FyD (fyd_at_u-picardie.fr)
Date: Tue Jun 27 2006 - 06:19:08 CDT

Quoting Miguel Ferreira <tetrass_at_hotmail.com>:

> I have several complexes protein-ligand (protein is the same in all of
> them), with a total charge of -1. For some of them leap assign the correct
> charge and hence, is able to neutralize the total charge, but for others,
> leap says the charge is -0,9995 or -0,9997.

RESP generates the charge value of each atom with an accuracy of +/-.0001.
Consequently, the sum of these 'inaccuracies' becomes +/- .0005 (maximum) for a
whole LEaP unit.

This is because of the rounding off procedure used in AMBER FF topology DB i.e.
because of using four digits after the decimal point. For a LEaP unit, the max
'inaccuracy' value because of rounding off is +/-.0005 if you use 4 digits, and
+/-.000005 if you use 6 digits...

To avoid the corresponding LEaP warnings (not a big deal anyway), we usually
manually correct a few atomic charge values within a LEaP unit with the
+/-.0001 value (since the accuracy of RESP is +/-.0001), to get a perfect
integer value for the total charge of a unit. This is quite simple to do for a
single unit.

However, this is a little more tricky for DNA and/or RNA FF topology DB since
some charge values (those of ribose and deoxyribose but C1' and H1') of all the
units are identical.... See the R.E.DD.B. project "F-60" where all the 32 RNA
and DNA nucleotides present the following total charges:
- Central unit total charge = -1.0000
- Terminal-5' unit + terminal-3' unit total charge = -1.0000
- Nucleoside total charge = 0.0000

regards, Francois

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