Dear David and AMBER users,
The DNA molecule has the phosphate groups on its 5' ends.
And I suspect that non-integral charge originates from that.
The OHE residue was created accordingly.
This is how one 5'-end looks like:
MODEL 1
HETATM 1 O OHE A 1 -2.273 -8.313 -1.809 1.00 0.00
O
HETATM 2 H OHE A 1 -2.030 -8.446 -0.861 1.00 0.00
H
HETATM 3 P DT A 2 -0.819 -8.604 -2.581 1.00 0.00
P
HETATM 4 OP1 DT A 2 -0.816 -7.797 -4.046 1.00 0.00
O1-
HETATM 5 OP2 DT A 2 -0.618 -10.237 -2.827 1.00 0.00
O
HETATM 6 O5' DT A 2 0.423 -8.007 -1.635 1.00 0.00
O
HETATM 7 C5' DT A 2 1.429 -7.769 -2.593 1.00 0.00
C
HETATM 8 C4' DT A 2 2.670 -7.211 -1.915 1.00 0.00
C
HETATM 9 O4' DT A 2 2.538 -5.761 -1.810 1.00 0.00
O
HETATM 10 C1' DT A 2 2.250 -5.395 -0.468 1.00 0.00
C
HETATM 11 N1 DT A 2 1.010 -4.500 -0.436 1.00 0.00
N
HETATM 12 C6 DT A 2 -0.268 -4.992 -0.479 1.00 0.00
C
HETATM 13 C5 DT A 2 -1.329 -4.177 -0.394 1.00 0.00
C
HETATM 14 C7 DT A 2 -2.732 -4.706 -0.440 1.00 0.00
C
HETATM 15 C4 DT A 2 -1.157 -2.754 -0.255 1.00 0.00
C
HETATM 16 O4 DT A 2 -2.068 -1.932 -0.171 1.00 0.00
O
HETATM 17 N3 DT A 2 0.161 -2.348 -0.221 1.00 0.00
N
HETATM 18 C2 DT A 2 1.273 -3.161 -0.306 1.00 0.00
C
HETATM 19 O2 DT A 2 2.405 -2.707 -0.266 1.00 0.00
O
HETATM 20 C3' DT A 2 2.911 -7.677 -0.478 1.00 0.00
C
HETATM 21 C2' DT A 2 2.089 -6.682 0.343 1.00 0.00
C
HETATM 22 O3' DT A 2 4.249 -7.615 -0.007 1.00 0.00
O
HETATM 23 H5' DT A 2 1.069 -7.051 -3.329 1.00 0.00
H
HETATM 24 H5'' DT A 2 1.684 -8.704 -3.092 1.00 0.00
H
HETATM 25 H4' DT A 2 3.535 -7.360 -2.561 1.00 0.00
H
HETATM 26 H1' DT A 2 3.036 -4.739 -0.093 1.00 0.00
H
HETATM 27 H6 DT A 2 -0.435 -6.057 -0.538 1.00 0.00
H
HETATM 28 H71 DT A 2 -2.887 -5.399 0.387 1.00 0.00
H
HETATM 29 H72 DT A 2 -3.436 -3.878 -0.356 1.00 0.00
H
HETATM 30 H73 DT A 2 -2.894 -5.226 -1.384 1.00 0.00
H
HETATM 31 H3 DT A 2 0.343 -1.278 -0.117 1.00 0.00
H
HETATM 32 H3' DT A 2 2.503 -8.680 -0.348 1.00 0.00
H
HETATM 33 H2' DT A 2 1.332 -7.219 0.915 1.00 0.00
H
HETATM 34 H2'' DT A 2 2.746 -6.144 1.027 1.00 0.00
H
With O instead of -O1 for the OP1 atom the result was the same.
This DNA double-helix was created using NAB,
then the phosphate groups were added manually via Schrodinger Maestro,
then I renamed DT5 to DT and created OHE residue, some atoms were
re-grouped and renamed
and the resulted PDB was passed through the pdb4amber.
The 3' ends have not been changed after NAB and remained as by default.
Thank you in advance,
Nick
On Mon, Feb 19, 2018, Nikolay N. Kuzmich wrote:
>
> when checking the charge of a DNA model tleap reports error that the
> unperturbed charge
> of the unit is -64.172.
We would need to know details of how you constructed the DNA model: if you
have 5' and 3' units on the ends, the charge should be integral (and equal
to
the number of phosphate groups.) You are right to be concerned, but
resolution depends on exactly what you did.
....dac
Dear AMBER users and developers,
when checking the charge of a DNA model tleap reports error that the
unperturbed charge
of the unit is -64.172. I performed the google search on the topic and
found out that it is just a warning. But from another hand that means it is
impossible to fully neutralize the system
and the residul charge may lead to unrealistic behaviour.
The AmberTools15 is used.
What should be done in this situation?
Sincerely,
Nick
Nikolay Kuzmich
Department of Drug Safety,
Research Institute of Influenza,
WHO National Influenza Centre of Russia,
15/17 Professor Popov St.,
Saint-Petersburg
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Received on Wed Feb 21 2018 - 01:30:02 PST
