Thank you for the suggestions.
I am trying with the LISTOUT=POUT command. It shows high penalties in many
cases. Then I put the values for rk2 and rk3 in DIST file as 0 andd 32,
ialtd=1 (as read in advanced/tutorial4-AMBER refinement of duplex DNA).
Then I got the values as shown below (I introduced the distances for one
strand only now).
Restraints, deviations, and energy contributions: pencut = -0.00
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
H1' DC5 1 -- H2' DC5 1: 2.320 2.000 0.320 3.267 d
0: 0
H1' DC5 1 -- H6 DC5 1: 3.466 3.270 0.196 1.226 d
0: 0
H2' DC5 1 -- H1' DC5 1: 2.320 2.470 0.000 0.000 d
0: 0
H2' DC5 1 -- H6 DC5 1: 2.225 3.620 0.000 0.000 d
0: 0
H2' DC5 1 -- H6 DC 2: 2.259 4.000 0.000 0.000 d
0: 0
H2' DC5 1 -- H6 DC5 1: 2.225 2.720 0.000 0.000 d
0: 0
H2'' DC5 1 -- H6 DC 2: 3.531 3.490 0.041 0.053 d
0: 0
H41 DC5 1 -- H5 DC 2: 2.689 2.620 0.069 0.154 d
0: 0
H41 DC5 1 -- H42 DC5 1: 1.678 1.480 0.198 1.259 d
0: 0
H41 DC5 1 -- H5 DC 2: 2.689 2.620 0.069 0.154 d
0: 0
H2' DC 2 -- H1' DC 2: 2.915 3.290 0.000 0.000 d
0: 0
H2' DC 2 -- H6 DC 2: 2.134 1.960 0.174 0.968 d
0: 0
H2' DC 2 -- H8 DA 3: 3.211 3.030 0.181 1.044 d
0: 0
H2'' DC 2 -- H1' DC 2: 2.137 2.720 0.000 0.000 d
0: 0
H2'' DC 2 -- H2' DC 2: 1.778 1.800 0.022 0.000 d
0: 0
H2'' DC 2 -- H6 DC 2: 3.250 3.500 0.000 0.000 d
0: 0
H2'' DC 2 -- H8 DA 3: 2.565 2.700 0.000 0.000 d
0: 0
H5 DC 2 -- H6 DC 2: 2.386 2.480 0.000 0.000 d
0: 0
H5 DC 2 -- H41 DC 2: 3.717 3.600 0.117 0.441 d
0: 0
H6 DC 2 -- H2' DC 2: 2.134 2.000 0.134 0.574 d
0: 0
H6 DC 2 -- H5 DC 2: 2.386 2.220 0.166 0.880 d
0: 0
H42 DC 2 -- H5 DC 2: 2.445 3.600 0.000 0.000 d
0: 0
H42 DC 2 -- H41 DC 2: 1.757 1.600 0.157 0.785 d
0: 0
H1' DA 3 -- H2' DA 3: 2.838 2.670 0.168 0.908 d
0: 0
H1' DA 3 -- H8 DA 3: 3.222 3.220 0.002 0.000 d
0: 0
H2' DA 3 -- H1' DA 3: 2.838 2.800 0.038 0.047 d
0: 0
H2' DA 3 -- H8 DA 3: 2.094 2.020 0.074 0.177 d
0: 0
H2'' DA 3 -- H1' DA 3: 1.946 1.400 0.546 9.336 d
0: 0
H2'' DA 3 -- H8 DA 3: 2.906 3.000 0.000 0.000 d
0: 0
H8 DA 3 -- H1' DC 2: 3.415 3.150 0.265 2.255 d
0: 0
H8 DA 3 -- H6 DC 2: 3.119 3.150 0.000 0.000 d
0: 0
H8 DA 3 -- H2' DA 3: 2.094 1.950 0.144 0.667 d
0: 0
H1' DA 4 -- H1' DA 3: 1.848 1.510 0.338 3.666 d
0: 0
H1' DA 4 -- H8 DA 3: 3.532 3.080 0.452 6.538 d
0: 0
H1' DA 4 -- *H73 DT 5: 4.210 4.020 0.190 1.150 d
0: 0
H1' DA 4 -- H6 DT 5: 3.493 3.360 0.133 0.562 d
0: 0
H2 DA 4 -- H61 DA 3: 2.334 2.300 0.034 0.036 d
0: 0
H2 DA 4 -- H62 DA 3: 3.387 3.570 0.000 0.000 d
0: 0
H2 DA 4 -- H3 DT 5: 2.669 2.880 0.000 0.000 d
0: 0
H2' DA 4 -- H1' DA 4: 3.058 2.800 0.258 2.126 d
0: 0
H2' DA 4 -- H8 DA 4: 2.088 2.160 0.000 0.000 d
0: 0
H2' DA 4 -- *H73 DT 5: 2.518 3.530 0.000 0.000 d
0: 0
H2' DA 4 -- H6 DT 5: 2.983 2.910 0.073 0.169 d
0: 0
H2'' DA 4 -- H1' DA 4: 2.392 2.330 0.062 0.125 d
0: 0
H2'' DA 4 -- H2' DA 4: 1.851 2.000 0.000 0.000 d
0: 0
H2'' DA 4 -- H8 DA 4: 3.539 3.500 0.039 0.049 d
0: 0
H2'' DA 4 -- *H73 DT 5: 3.353 3.390 0.000 0.000 d
0: 0
H2'' DA 4 -- H6 DT 5: 2.140 2.510 0.000 0.000 d
0: 0
H8 DA 4 -- H1' DA 3: 4.318 3.500 0.818 14.216 d
0: 0
H8 DA 4 -- H1' DA 4: 3.312 3.100 0.212 1.437 d
0: 0
H8 DA 4 -- H2' DA 4: 2.088 2.040 0.048 0.073 d
0: 0
H8 DA 4 -- *H73 DT 5: 2.925 2.950 0.000 0.000 d
0: 0
*H73 DT 5 -- H2' DA 4: 2.518 3.540 0.000 0.000 d
0: 0
*H73 DT 5 -- H8 DA 4: 2.925 4.200 0.000 0.000 d
0: 0
*H73 DT 5 -- H6 DT 5: 2.552 3.000 0.000 0.000 d
0: 0
H1' DT 5 -- H6 DT 5: 3.618 3.470 0.148 0.703 d
0: 0
H1' DT 5 -- *H73 DT 6: 4.203 3.930 0.273 2.382 d
0: 0
H2' DT 5 -- H6 DT 5: 1.943 2.210 0.000 0.000 d
0: 0
H2'' DT 5 -- H1' DT 5: 2.173 1.970 0.203 1.318 d
0: 0
H2'' DT 5 -- H2' DT 5: 1.740 1.800 0.060 0.000 d
0: 0
H2'' DT 5 -- H6 DT 5: 3.000 2.630 0.370 4.382 d
0: 0
H2'' DT 5 -- H6 DT 6: 2.289 2.490 0.000 0.000 d
0: 0
H6 DT 5 -- H8 DA 4: 4.253 4.100 0.153 0.749 d
0: 0
H6 DT 5 -- *H73 DT 5: 2.552 2.590 0.000 0.000 d
0: 0
*H73 DT 6 -- *H73 DT 5: 3.332 3.560 0.000 0.000 d
0: 0
*H73 DT 6 -- H2'' DT 5: 2.701 2.520 0.181 1.046 d
0: 0
*H73 DT 6 -- H6 DT 5: 3.163 3.840 0.000 0.000 d
0: 0
*H73 DT 6 -- H1' DT 6: 4.424 4.080 0.344 3.792 d
0: 0
*H73 DT 6 -- H6 DT 6: 2.493 2.470 0.023 0.017 d
0: 0
H1' DT 6 -- H6 DT 6: 2.755 2.980 0.000 0.000 d
0: 0
H2' DT 6 -- H1' DT 6: 2.654 2.580 0.074 0.176 d
0: 0
H2' DT 6 -- H2'' DT 6: 1.689 1.800 0.111 0.000 d
0: 0
H2' DT 6 -- H6 DT 6: 2.009 2.000 0.009 0.003 d
0: 0
H2' DT 6 -- H8 DG 7: 1.840 3.100 0.000 0.000 d
0: 0
H2'' DT 6 -- H1' DT 6: 1.899 4.200 0.000 0.000 d
0: 0
H2'' DT 6 -- H2' DT 6: 1.689 1.800 0.111 0.000 d
0: 0
H2'' DT 6 -- H6 DT 6: 3.058 3.300 0.000 0.000 d
0: 0
H2'' DT 6 -- H8 DG 7: 2.397 3.000 0.000 0.000 d
0: 0
H6 DT 6 -- H2'' DT 5: 2.289 2.100 0.189 1.137 d
0: 0
H6 DT 6 -- *H73 DT 6: 2.493 2.410 0.083 0.219 d
0: 0
H6 DT 6 -- H1' DT 6: 2.755 2.470 0.285 2.604 d
0: 0
H6 DT 6 -- H2' DT 6: 2.009 2.100 0.000 0.000 d
0: 0
H6 DT 6 -- H2'' DT 6: 3.058 2.850 0.208 1.387 d
0: 0
H1' DG 7 -- H2' DG 7: 2.789 2.400 0.389 4.848 d
0: 0
H1' DG 7 -- H8 DG 7: 3.557 3.200 0.357 4.089 d
0: 0
H2'' DG 7 -- H1' DG 7: 2.101 2.200 0.000 0.000 d
0: 0
H2'' DG 7 -- H8 DG 7: 3.759 3.500 0.259 2.140 d
0: 0
H2'' DG 7 -- H8 DG3 8: 3.134 2.830 0.304 2.961 d
0: 0
H8 DG 7 -- H2' DT 6: 1.840 1.000 0.840 14.474 d
0: 0
H8 DG 7 -- H2' DT 6: 1.840 2.000 0.000 0.000 d
0: 0
H8 DG 7 -- H2' DG 7: 2.135 2.000 0.135 0.586 d
0: 0
H21 DG 7 -- H8 DG3 8: 3.019 2.940 0.079 0.201 d
0: 0
H1' DG3 8 -- H2' DG3 8: 2.806 2.860 0.000 0.000 d
0: 0
H1' DG3 8 -- H2'' DG3 8: 2.196 2.510 0.000 0.000 d
0: 0
H1' DG3 8 -- H8 DG3 8: 3.101 2.920 0.181 1.053 d
0: 0
H2' DG3 8 -- H1' DG3 8: 2.806 2.300 0.506 8.191 d
0: 0
H2' DG3 8 -- H8 DG3 8: 2.430 2.420 0.010 0.003 d
0: 0
H8 DG3 8 -- H1' DG 7: 2.973 2.620 0.353 3.979 d
0: 0
H8 DG3 8 -- H2' DG3 8: 2.430 2.290 0.140 0.623 d
0: 0
H8 DG3 8 -- H2'' DG3 8: 2.161 2.010 0.151 0.727 d
0: 0
H22 DG3 8 -- H1' DG 7: 2.963 2.620 0.343 3.767 d
0: 0
Total distance penalty: 121.899
How the penalties are calculated? In some cases the penalty is 0, though
there is a difference between the target and current values.
For a valid structure what should be the range of penality ?
Regards,
Maya
On Thu, Jan 2, 2020 at 7:11 PM David Case <david.case.rutgers.edu> wrote:
> On Thu, Jan 02, 2020, maya nair wrote:
>
> >I am trying to do the NMR restrained MD for a DNA-ligand complex. I
> started
> >with a docked structure. Minimized it and the MD was run . When adding
> >distance file, the structure is getting very much distorted. I followed
> the
> >tutorial A4 in structure refinement in Amber and also followed the MD
> >tutorial and added dist file into them. But my structure is getting
> >distorted. What are the precautions to be taken to avoid this/ Can you
> give
> >some suggestions to workout this?
>
> Use the LISTOUT=POUT command command to see the violations you are
> getting for each individual distance. Are most satistified, but just a
> few are bad? Is everything bad? Can you do a trial calculation with
> just a few distance restraints, and gradually add more to see which ones
> might be causing the problem?
>
> If you have lots of restraints, the "sviol" program will format the
> info into a nicer format, making it easier to visualize. This is
> helpful if most the of restraints are being satisfied, and only a few
> are causing problems. It is less useful if basically all the restraints
> are causing problems.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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Received on Mon Jan 06 2020 - 04:30:02 PST
