Quoting jitrayut jitonnom <jitrayut.018.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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Received on Wed Jun 21 2006 - 06:07:08 PDT
