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From: FyD <fyd.u-picardie.fr>

Date: Tue, 27 Jun 2006 13:19:08 +0200

Quoting Miguel Ferreira <tetrass.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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Received on Wed Jun 28 2006 - 06:07:05 PDT

Date: Tue, 27 Jun 2006 13:19:08 +0200

Quoting Miguel Ferreira <tetrass.hotmail.com>:

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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Received on Wed Jun 28 2006 - 06:07:05 PDT

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