Hi,
I am trying to make a prep file for a guanine (RNA) , which will have additional phospate group bonded to the O2' and O3' atom. I made parametrization etc. but leap is trying to connect phosphor atoms with eachother. I have deffined loop for atoms O2' and P2 and I added 4 inproper dihedrals, but it still not work as it should. Please help me. The prep file:
0 0 0
leap-generated prep residue
Gcp.res
Gcp INT 0
CHANGE NOMIT DU BEG
0.00000
1 DUMM DU M 0.000000 0.000000 0.000000 0.0
2 DUMM DU M 1.000000 0.000000 0.000000 0.0
3 DUMM DU M 1.000000 1.000000 0.000000 0.0
4 P P M -3.635180 -2.496920 2.875670 0.170080
5 OP1 O2 E -3.905760 -4.070500 2.184120 -0.563385
6 OP2 O2 E -3.183450 -2.667890 4.547280 -0.563385
7 O5' OS M -2.357707 -1.694285 2.008810 0.065573
8 C5' CI M -2.140730 -0.432440 2.563358 -0.156161
9 H5' H1 E -2.067545 -0.497608 3.648132 0.062085
10 H5'' H1 E -2.999782 0.180699 2.320994 0.062085
11 C4' CT M -0.887487 0.232805 2.028409 -0.493664
12 H4' H1 E -0.704022 1.151870 2.576781 0.121779
13 O4' OS S 0.208417 -0.684846 2.244943 -0.425093
14 C1' CT 3 1.174238 -0.678000 1.202037 0.019100
15 H1' H2 E 2.140584 -0.575845 1.666596 0.200600
16 C2' CT B 0.728522 0.540656 0.413842 1.222645
17 H2' H1 E 1.061032 1.393714 1.004202 -0.589204
18 O2' OS E 0.982648 0.769841 -0.916908 -0.935987
20 N9 N* B 1.194173 -1.935319 0.481862 0.049200
21 C4 CB B 1.738009 -3.076498 0.975676 0.122200
22 C5 CB B 1.573230 -4.027834 0.009021 0.174400
23 C6 C B 2.052208 -5.357109 0.254490 0.477000
24 O6 O E 2.012778 -6.351117 -0.411306 -0.559700
25 N1 NA B 2.656822 -5.418622 1.533051 -0.478700
26 H1 H E 2.936141 -6.335043 1.809468 0.342400
27 C2 CA S 2.776961 -4.388326 2.409976 0.765700
28 N2 N2 B 3.368634 -4.693007 3.612999 -0.967200
29 H21 H E 4.146139 -5.316374 3.571586 0.436400
30 H22 H E 3.554147 -3.875878 4.154206 0.436400
31 N7 NB E 0.938215 -3.490059 -1.086865 -0.570900
32 N3 NC E 2.348705 -3.201804 2.185746 -0.632300
33 C8 CP S 0.732164 -2.263011 -0.783739 0.137400
34 H8 H5 E 0.279646 -1.532968 -1.420940 0.164000
35 C3' CT M -0.767674 0.455599 0.539670 1.947539
36 H3' H1 E -1.153897 -0.423661 0.035589 -0.430909
37 O3' OS M -1.196900 1.599438 -0.112836 -1.174128
4 P2 P B -0.314380 1.678614 -1.547100 1.660309
5 OP3 O2 E 0.105180 3.062383 -1.752330 -0.894038
6 OP4 O2 E -0.954188 0.823711 -2.549976 -0.894038
LOOP
C2' C3'
O2' P2
C2 N3
C8 N7
IMPROPER
C4 C8 N9 C1'
H8 N9 C8 N7
C6 C4 C5 N7
C5 N1 C6 O6
C6 C2 N1 H1
N2 N1 C2 N3
C2 H21 N2 H22
C5 N9 C4 N3
C2' O2' P2 OP3
C2' O2' P2 OP4
C3' O3' P2 OP4
C3' O3' P2 OP3
DONE
STOP
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 28 2023 - 03:00:02 PDT
