Dear all,
I have a non standard residue where adenosine has been modified to N6-threonylcarbamoyladenosine. I combine ESP of two molecules(DMP and modified nucleoside) to calculate the point charges of the modified nucleotide.I set inter-molecular charge constraints between the two Dimethylphosphate methyl atoms and the HO3' and HO5' hydroxyl atoms of a nucleoside. But I find that the charge of these six atoms after RESP2 fit is not zero. So when I build the central fragment of a modified nucleotide, the sum of charge is not integral. Another problem is that the connect is wrong. I have no idea how to solve these problems.
6 0.000000
1 6 1 8 1 9 1 10 2 21 2 34
6 0.000000
1 7 1 11 1 12 1 13 2 22 2 36
Point Charges Before & After Optimization
1
no. At.no. q(init) q(opt) ivary d(rstr)/dq
6 6 0.280463 0.280463 -1 0.003358
7 6 0.204837 0.204837 -1 0.004387
8 1 -0.036422 -0.036422 -1 0.000000
9 1 -0.004260 -0.004260 -1 0.000000
10 1 -0.026177 -0.026177 -1 0.000000
11 1 -0.004571 -0.004571 -1 0.000000
12 1 0.015549 0.015549 -1 0.000000
13 1 -0.020119 -0.020119 -1 0.000000
2
21 8 -0.682595 -0.682595 -1 0.001450
22 8 -0.588242 -0.588242 -1 0.001676
34 1 0.445782 0.445782 -1 0.000000
49 1 0.392933 0.392933 -1 0.000000
Joining U5 - U
Joining U - A
Joining A - C
Joining C - U
Joining U - U
Joining U - U
Joining U - G
Joining G - A
Joining A - U
One sided connection. Residue: default_name missing connect0 atom.
One sided connection. Residue: default_name missing connect1 atom.
Joining G - A
Joining A - G
Joining G - U
Joining U - A
Joining A - A3
ERROR: The unperturbed charge of the unit: -17.111177 is not integral.
WARNING: The unperturbed charge of the unit: -17.111177 is not zero.
Thank you in advance,
Xiaoting Mao
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Received on Fri Apr 12 2019 - 06:30:05 PDT
