AMBER Archive (2006)

Subject: Re: AMBER: LEaP error : unbalanced charge

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Jun 19 2006 - 02:03:38 CDT

Quoting jitrayut jitonnom <jitrayut.018_at_gmail.com>:

> I am studying the protonation state of heptapeptide binding with enzyme. In
> this work, I also used RESP charge model to calculate deprotonate tyrosine.
> But I found 1 error about total charge (-17.4815 ,do not add Na+ yet) when I
> do LEaP. So, my question is "Can I balance this charge to zero ?", if
> not, it means that this charge can be ignored right ? Or maybe someone can
> help me solve this problem.

Here you must understand & correct the problem... This is NOT normal.

Did you check that the total charge of your new residue = zero ?

To do it using LEaP for the 'already existing' unit ALA:
 xleap -f leaprc.ff98
 edit ALA
 Unit/Calculate net charge (LEaP pulldown)

You get such messages (bottom of the window):
Unit Editor: Total unperturbed charge: 0.000000
Unit Editor: Total perturbed charge: 0.000000

You can also use your calculator to do _manually_ the sum...

If you use an intra-molecular charge constraint set to zero during the fit, you
_have to_ check (always with your calculator this time) that after the fit the
sum of the charges of the set of atoms involved in the intra-molecular charge
constraint equals indeed zero.

If not, this means that the way you built your RESP input is wrong. A classical
error is that when nmol=1 (see RESP input/manual) you _cannot_ jump a line
_before_ the writing of the intra-molecular charge constraint in the input. On
the contrary, if nmol>1, you _have_ to jump a single line. I wonder if this is
clear in the RESP manual. This is a classical error done in RESP inputs.

In R.E.DD.B., projects often involve nmol>1. Consequently, you are going to find
inputs with an empty line before the intra-molecular charge constraint setting
section.

An example of intra-molecular charge constraint = 0 and nmol=1 is available @
/usr/local/amber8/examples/resp_charge_fit/peptoid
See the esp_stage1.in file:

 first stage of RESP. Peptoid for resp charge calculations
 &cntrl
 qwt=0.0005, nmol=1, ihfree=1
 &end
  1.0
 peptoid for resp charge calculations
    0 22
    1 0
    6 0
    1 0
    1 0
    6 0
    8 0
    7 0
    6 0
    1 0
    1 0
    1 0
    6 0
    1 0
    1 0
    6 0
    8 0
    7 0
    1 0
    6 0
    1 0
    1 0
    1 0 !!!! Do not jump a line here
    6 0.0 !!!! and jump a line if nmol>1
    1 1 1 2 1 3 1 4 1 5 1 6
    6 0.0
    1 17 1 18 1 19 1 20 1 21 1 22
    1 0.59730 as in the whole AA database
    1 15
    1 -0.56790 as in the whole AA database
    1 16

regards, Francois

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