AMBER: xLeAP: TI calculation: the perturbed charge is not integral

From: Ignacio Faustino <>
Date: Wed, 21 Mar 2007 20:17:12 +0100

Dear AMBER users,

I am trying to do an MD/TI calculation for a mutated nucleotide and for
this purpose we have prepared the corresponding frcmod file for both
unperturbed and perturbed systems. Once I have calculated the atomic
charges for both systems, I set the charges and delta charges into the
corresponding columns in the editor table in xLeAP. My perturbation
does not involve dummy atoms but substitution of two atoms (I have
attached the editor table). Since the molecule is small enough I have
calculated the net charge by summing by hand the atomic charges for both
systems and they are equal. But when I try to "check" the systems what I
receive from xLeAP is:

Unit Editor: WARNING: The unperturbed charge of the unit: -1.000000 is
not zero.
Unit Editor: ERROR: The perturbed charge: -0.275000 is not integral.
Unit Editor: WARNING: The perturbed charge: -0.275000 is not zero.

Besides this, when I return to the editor table I try to change the
delta charge of every atom that is not involved in substitution (e.g.,C7
CT), and there is no change in the perturbed charge when I save and
check. But if I do the same with every three atoms with assigned as
"true", the perturbed charge changes. It seems that the changes in
"true" atoms influence in net charge of perturbed system. And I can not
replace "true" by nothing while there is a change in the PERT.type
column and it seems that xLeAP put it by default.

I am using amber 8.0 and any suggestions will be highly appreciated.


I. Faustino

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Received on Sun Mar 25 2007 - 06:07:16 PDT
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