Dear Jena,
I have a non standard residue where adenosine has been modified to N6-threonylcarbamoyladenosine. I read the AMBER mailing list
http://archive.ambermd.org/201002/0013.html ,and I have some questions. I am confused how to generate the RESP charges. I was wondering if you could kindly send me the details of information about how to get the point charges for 6OG, including Gaussian input ,output files, resp input, output files and so on.
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. If it is convenient, can you help me find out what is wrong ?
Steps:
1.Charge Derivation for the modified nucleotide.
1.1 optimize geometry for dimethylphosphate(DMP) and modified nucleoside
1.2 calculate electrostatic potentials(ESP) for dimethylphosphate(DMP) and modified nucleoside
1.3 convert the Gaussian ESP data into the RESP format
command: espgen -i DMP_esp.out -o DMP.esp
espgen -i t6A_side_esp.out -o t6A_side.esp
cat DMP.esp t6A_side.esp> t6A_tide_esp1.esp
1.4 run the RESP fit
I set inter-molecular charge constraints between the two Dimethylphosphate methyl atoms and the HO3' and HO5' hydroxyl atoms of a nucleoside. I also set the equivalent of sugar atoms that a modified nucleoside to a normal nucleoside, and some other constraints.
command1:resp -O -i t6A_resp1.in -o t6A_resp1.out -p t6A_resp1.pch -t t6A_resp1.chg -q t6A_resp1.qin -e t6A_tide_esp1.esp
command2:resp -O -i t6A_resp2.in -o t6A_resp2.out -p t6A_resp2.pch -t t6A_resp2.chg -q t6A_resp1.chg -e t6A_tide_esp1.esp
t6A-RESP1 RUN #1
&cntrl
nmol=2,
ihfree=1,
qwt=0.0005,
iqopt=2,
/
1.0
DMP
-1 13
15 -1
8 -1
8 -1
8 -1
8 -1
6 0
6 0
1 0
1 0
1 0
1 0
1 0
1 0
1.0
t6A
-1 48
7 0
7 0
7 0
7 0
7 0
7 0
6 -1
6 -1
6 -1
6 0
6 0
6 0
6 0
6 0
6 0
6 0
6 0
6 0
6 0
8 -1
8 0
8 0
8 0
8 0
8 0
8 0
6 -1
8 -1
6 -1
1 -1
1 -1
1 -1
1 -1
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 -1
1 -1
1 -1
Intra and/or inter-molecular charge restraints for atom or group of atoms
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
t6A
Point Charges Before & After Optimization
no. At.no. q(init) q(opt) ivary d(rstr)/dq
1 15 1.166200 1.166200 -1 0.000427
2 8 -0.776000 -0.776000 -1 0.000639
3 8 -0.776000 -0.776000 -1 0.000639
4 8 -0.498900 -0.498900 -1 0.000983
5 8 -0.524600 -0.524600 -1 0.000936
6 6 0.000000 0.280463 0 0.001679
7 6 0.000000 0.204837 0 0.002194
8 1 0.000000 -0.036422 0 0.000000
9 1 0.000000 -0.004260 0 0.000000
10 1 0.000000 -0.026177 0 0.000000
11 1 0.000000 -0.004571 0 0.000000
12 1 0.000000 0.015549 0 0.000000
13 1 0.000000 -0.020119 0 0.000000
14 7 0.000000 -0.249226 0 0.001862
15 7 0.000000 -0.565783 0 0.000870
16 7 0.000000 -0.660810 0 0.000748
17 7 0.000000 -0.633745 0 0.000779
18 7 0.000000 -0.467952 0 0.001045
19 7 0.000000 -0.619038 0 0.000797
20 6 0.202200 0.202200 -1 0.002217
21 6 0.106500 0.106500 -1 0.003423
22 6 0.055800 0.055800 -1 0.004366
23 6 0.000000 0.520048 0 0.000944
24 6 0.000000 0.263689 0 0.001773
25 6 0.000000 0.017577 0 0.004925
26 6 0.000000 0.539716 0 0.000911
27 6 0.000000 0.459254 0 0.001064
28 6 0.000000 0.770757 0 0.000643
29 6 0.000000 0.045717 0 0.004547
30 6 0.000000 0.788226 0 0.000629
31 6 0.000000 0.289652 0 0.001632
32 6 0.000000 -0.245641 0 0.001885
33 8 -0.354800 -0.354800 -1 0.001356
34 8 0.000000 -0.682595 0 0.000725
35 8 0.000000 -0.588242 0 0.000838
36 8 0.000000 -0.773669 0 0.000641
37 8 0.000000 -0.775197 0 0.000640
38 8 0.000000 -0.565972 0 0.000870
39 8 0.000000 -0.679583 0 0.000728
40 6 0.067000 0.067000 -1 0.004154
41 8 -0.613900 -0.613900 -1 0.000804
42 6 0.039400 0.039400 -1 0.004652
43 1 0.061500 0.061500 -1 0.000000
44 1 0.117400 0.117400 -1 0.000000
45 1 0.067900 0.067900 -1 0.000000
46 1 0.067900 0.067900 -1 0.000000
47 1 0.000000 0.445782 0 0.000000
48 1 0.000000 0.105542 0 0.000000
49 1 0.000000 0.392933 0 0.000000
50 1 0.000000 0.064976 0 0.000000
51 1 0.000000 0.079596 0 0.000000
52 1 0.000000 0.321907 0 0.000000
53 1 0.000000 0.009644 0 0.000000
54 1 0.000000 0.015659 0 0.000000
55 1 0.000000 0.406936 0 0.000000
56 1 0.000000 0.089279 0 0.000000
57 1 0.000000 0.059962 0 0.000000
58 1 0.000000 0.287201 0 0.000000
59 1 0.097200 0.097200 -1 0.000000
60 1 0.418600 0.418600 -1 0.000000
61 1 0.200700 0.200700 -1 0.000000
ERROR: The unperturbed charge of the unit: -0.111177 is not integral.
WARNING: The unperturbed charge of the unit: -0.111177 is not zero.
Best regards,
Xiaoting
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Received on Sat Apr 13 2019 - 03:00:03 PDT
