AMBER Archive (2006)Subject: Re: AMBER: Leap: neutralising the charge
From: FyD (fyd_at_upicardie.fr)
Date: Tue Jun 27 2006  06:19:08 CDT
Quoting Miguel Ferreira <tetrass_at_hotmail.com>:
> I have several complexes proteinligand (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 "F60" where all the 32 RNA
and DNA nucleotides present the following total charges:
 Central unit total charge = 1.0000
 Terminal5' unit + terminal3' unit total charge = 1.0000
 Nucleoside total charge = 0.0000
regards, Francois

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