Hi, Case,
Thanks for u reply!
The minimisation stage 2- minimising the entire system results is as follows:
“ FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2500 -1.5472E+05 5.3890E-01 3.1856E+01 H1 26328
BOND = 11197.6011 ANGLE = 293.1576 DIHED = 878.3573
VDWAALS = 28137.6817 EEL = -191368.2955 HBOND = 0.0000
1-4 VDW = 343.3582 1-4 EEL = -4205.1036 RESTRAINT = 0.0000”
I think "VDWAALS = 28137.6817 , 1-4 VDW = 343.3582" it is high which represents the bad contacts in water and RNA and cannot drop when run minimisation stage 2. Please see the the minimisation stage 2 results:
" 4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 11326322
| TOTAL SIZE OF NONBOND LIST = 11326322
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4242E+05 9.5310E+00 5.7378E+02 N1 401
BOND = 9547.2956 ANGLE = 337.2569 DIHED = 961.3540
VDWAALS = 22585.4504 EEL = -172449.9513 HBOND = 0.0000
1-4 VDW = 563.0988 1-4 EEL = -3963.6343 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -1.4548E+05 7.4152E-01 4.8552E+01 C2 403
BOND = 9498.3454 ANGLE = 332.0011 DIHED = 919.3145
VDWAALS = 20835.8872 EEL = -173220.2579 HBOND = 0.0000
1-4 VDW = 387.9215 1-4 EEL = -4229.1150 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -1.4595E+05 1.1804E+00 7.9712E+01 C2 403
BOND = 9558.2153 ANGLE = 330.2509 DIHED = 911.7633
VDWAALS = 21023.3414 EEL = -173881.5118 HBOND = 0.0000
1-4 VDW = 361.3785 1-4 EEL = -4258.2718 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -1.4632E+05 7.2487E-01 3.5699E+01 C2 848
BOND = 9611.2070 ANGLE = 318.9279 DIHED = 908.2140
VDWAALS = 21227.4820 EEL = -174473.7577 HBOND = 0.0000
1-4 VDW = 352.2706 1-4 EEL = -4262.5470 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.4660E+05 1.1128E+00 6.6847E+01 C6 1227
BOND = 9673.1653 ANGLE = 321.1408 DIHED = 903.4749
VDWAALS = 21435.7044 EEL = -175020.1943 HBOND = 0.0000
1-4 VDW = 348.5184 1-4 EEL = -4265.2229 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
250 -1.4688E+05 6.0640E-01 2.8665E+01 C4 1236
BOND = 9700.6903 ANGLE = 324.3102 DIHED = 898.7963
VDWAALS = 21637.2956 EEL = -175518.9695 HBOND = 0.0000
1-4 VDW = 347.8185 1-4 EEL = -4270.6674 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -1.4713E+05 2.6399E-01 6.8544E+00 N9 1128
BOND = 9747.3160 ANGLE = 319.4256 DIHED = 894.5218
VDWAALS = 21826.6875 EEL = -175994.0300 HBOND = 0.0000
1-4 VDW = 345.2565 1-4 EEL = -4268.9668 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -1.4736E+05 3.1515E-01 1.1025E+01 N9 1128
BOND = 9792.0881 ANGLE = 318.6745 DIHED = 890.7609
VDWAALS = 22010.7191 EEL = -176450.1247 HBOND = 0.0000
1-4 VDW = 344.3839 1-4 EEL = -4268.1166 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -1.4758E+05 7.3770E-01 3.3519E+01 N9 1128
BOND = 9843.8519 ANGLE = 317.6246 DIHED = 887.5775
VDWAALS = 22188.3559 EEL = -176891.6442 HBOND = 0.0000
1-4 VDW = 342.8137 1-4 EEL = -4265.5803 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -1.4779E+05 3.9343E-01 1.8077E+01 N9 300
BOND = 9869.8832 ANGLE = 320.6362 DIHED = 884.9300
VDWAALS = 22357.0701 EEL = -177302.7604 HBOND = 0.0000
1-4 VDW = 344.5669 1-4 EEL = -4267.0180 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -1.4798E+05 6.1989E-01 2.9675E+01 N9 300
BOND = 9907.4804 ANGLE = 322.3144 DIHED = 882.9411
VDWAALS = 22512.3431 EEL = -177687.2436 HBOND = 0.0000
1-4 VDW = 345.0847 1-4 EEL = -4266.0683 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -1.4817E+05 2.1754E-01 3.8063E+00 N9 300
BOND = 9942.4230 ANGLE = 316.5213 DIHED = 881.5965
VDWAALS = 22655.2427 EEL = -178048.7134 HBOND = 0.0000
1-4 VDW = 343.6017 1-4 EEL = -4262.6475 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -1.4835E+05 6.0043E-01 3.4041E+01 C6 1227
BOND = 9983.4767 ANGLE = 314.9633 DIHED = 880.6932
VDWAALS = 22797.0403 EEL = -178407.6652 HBOND = 0.0000
1-4 VDW = 342.6502 1-4 EEL = -4260.0086 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
650 -1.4851E+05 8.2609E-01 4.5470E+01 C6 1227
BOND = 10020.6325 ANGLE = 314.2338 DIHED = 880.0666
VDWAALS = 22931.2605 EEL = -178744.8634 HBOND = 0.0000
1-4 VDW = 341.8729 1-4 EEL = -4258.1785 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -1.4869E+05 4.6919E-01 2.0748E+01 N9 300
BOND = 10037.5938 ANGLE = 317.4462 DIHED = 879.4580
VDWAALS = 23064.6906 EEL = -179074.0860 HBOND = 0.0000
1-4 VDW = 344.1792 1-4 EEL = -4259.4339 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
750 -1.4885E+05 2.1069E-01 4.8347E+00 N9 300
BOND = 10068.7843 ANGLE = 313.0910 DIHED = 878.8198
VDWAALS = 23190.0440 EEL = -179387.9514 HBOND = 0.0000
1-4 VDW = 343.1907 1-4 EEL = -4256.0842 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -1.4900E+05 3.8557E-01 1.7018E+01 N9 394
BOND = 10101.0761 ANGLE = 311.5324 DIHED = 878.2419
VDWAALS = 23315.4622 EEL = -179696.0173 HBOND = 0.0000
1-4 VDW = 342.6972 1-4 EEL = -4253.7369 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
850 -1.4914E+05 6.1268E-01 3.4967E+01 C4 951
BOND = 10133.2011 ANGLE = 310.1828 DIHED = 877.7565
VDWAALS = 23438.8122 EEL = -179993.7875 HBOND = 0.0000
1-4 VDW = 342.9088 1-4 EEL = -4251.8258 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
900 -1.4928E+05 1.8907E-01 3.9255E+00 N9 300
BOND = 10151.3912 ANGLE = 311.3546 DIHED = 877.3737
VDWAALS = 23559.0147 EEL = -180274.0910 HBOND = 0.0000
1-4 VDW = 343.3964 1-4 EEL = -4252.3370 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
950 -1.4941E+05 4.9152E-01 2.2844E+01 N9 300
BOND = 10177.6041 ANGLE = 312.6634 DIHED = 876.9806
VDWAALS = 23677.7503 EEL = -180547.8724 HBOND = 0.0000
1-4 VDW = 344.3196 1-4 EEL = -4252.1490 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.4954E+05 2.2821E-01 8.9939E+00 N9 300
BOND = 10203.6949 ANGLE = 308.4013 DIHED = 876.6579
VDWAALS = 23791.1985 EEL = -180809.9977 HBOND = 0.0000
1-4 VDW = 342.6881 1-4 EEL = -4249.4523 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1050 -1.5062E+05 6.8665E-01 3.9862E+01 H2 21142
BOND = 10476.4265 ANGLE = 309.8924 DIHED = 877.5391
VDWAALS = 25107.5841 EEL = -183494.7257 HBOND = 0.0000
1-4 VDW = 345.9187 1-4 EEL = -4239.0260 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1100 -1.5088E+05 4.5561E-01 2.5918E+01 O5' 1025
BOND = 10496.3996 ANGLE = 305.4788 DIHED = 876.7258
VDWAALS = 25227.4289 EEL = -183895.8666 HBOND = 0.0000
1-4 VDW = 344.3500 1-4 EEL = -4237.5564 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1150 -1.5109E+05 4.7551E-01 3.0468E+01 C6 809
BOND = 10529.2972 ANGLE = 303.4992 DIHED = 876.7103
VDWAALS = 25377.0389 EEL = -184282.2194 HBOND = 0.0000
1-4 VDW = 343.6759 1-4 EEL = -4235.5012 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1200 -1.5130E+05 6.4751E-01 2.9427E+01 C6 809
BOND = 10565.1704 ANGLE = 301.7878 DIHED = 877.1133
VDWAALS = 25538.7377 EEL = -184693.1777 HBOND = 0.0000
1-4 VDW = 343.3869 1-4 EEL = -4231.9883 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1250 -1.5166E+05 2.8855E-01 2.3518E+01 P 1022
BOND = 10627.5150 ANGLE = 292.7253 DIHED = 879.8502
VDWAALS = 25822.8769 EEL = -185407.3048 HBOND = 0.0000
1-4 VDW = 344.2053 1-4 EEL = -4224.6248 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1300 -1.5197E+05 3.5409E-01 1.2979E+01 H2 34312
BOND = 10692.7135 ANGLE = 291.8460 DIHED = 880.9654
VDWAALS = 26074.2752 EEL = -186028.0020 HBOND = 0.0000
1-4 VDW = 343.8146 1-4 EEL = -4222.5423 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1350 -1.5230E+05 4.4771E-01 2.5484E+01 O 18377
BOND = 10761.2644 ANGLE = 294.1933 DIHED = 881.5304
VDWAALS = 26341.7218 EEL = -186706.1334 HBOND = 0.0000
1-4 VDW = 344.5016 1-4 EEL = -4219.6723 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1400 -1.5249E+05 4.2067E-01 2.0973E+01 O 18377
BOND = 10792.9576 ANGLE = 295.4242 DIHED = 880.9108
VDWAALS = 26469.9620 EEL = -187055.0528 HBOND = 0.0000
1-4 VDW = 344.8805 1-4 EEL = -4219.9949 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1450 -1.5262E+05 3.4786E-01 2.8312E+01 P 258
BOND = 10809.7663 ANGLE = 294.0928 DIHED = 880.9074
VDWAALS = 26566.4353 EEL = -187300.1109 HBOND = 0.0000
1-4 VDW = 344.9203 1-4 EEL = -4218.9241 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1500 -1.5274E+05 3.4361E-01 1.6309E+01 C2' 822
BOND = 10839.4005 ANGLE = 293.9217 DIHED = 880.7981
VDWAALS = 26654.9871 EEL = -187539.5814 HBOND = 0.0000
1-4 VDW = 345.0779 1-4 EEL = -4218.4133 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1550 -1.5287E+05 3.3360E-01 1.9131E+01 P 258
BOND = 10845.4526 ANGLE = 293.7189 DIHED = 881.0950
VDWAALS = 26742.7187 EEL = -187763.3597 HBOND = 0.0000
1-4 VDW = 345.1545 1-4 EEL = -4217.3255 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1600 -1.5300E+05 3.0967E-01 1.9687E+01 P 258
BOND = 10864.9558 ANGLE = 293.6313 DIHED = 881.2769
VDWAALS = 26829.6665 EEL = -187991.5462 HBOND = 0.0000
1-4 VDW = 344.9796 1-4 EEL = -4217.9947 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1650 -1.5311E+05 2.7587E-01 1.8790E+01 O 18377
BOND = 10882.6063 ANGLE = 293.1063 DIHED = 881.6224
VDWAALS = 26907.5946 EEL = -188199.2276 HBOND = 0.0000
1-4 VDW = 344.5662 1-4 EEL = -4217.5497 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1700 -1.5327E+05 2.8182E-01 1.9873E+01 O 18377
BOND = 10925.3682 ANGLE = 293.3426 DIHED = 881.7371
VDWAALS = 27038.1092 EEL = -188537.0527 HBOND = 0.0000
1-4 VDW = 344.6985 1-4 EEL = -4217.5846 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1750 -1.5339E+05 2.6675E-01 2.3185E+01 O 18377
BOND = 10939.7985 ANGLE = 291.2723 DIHED = 881.6052
VDWAALS = 27129.9577 EEL = -188761.1639 HBOND = 0.0000
1-4 VDW = 344.2223 1-4 EEL = -4216.7462 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1800 -1.5349E+05 2.0935E-01 2.0863E+01 O 18377
BOND = 10956.0148 ANGLE = 290.9623 DIHED = 881.7962
VDWAALS = 27196.0179 EEL = -188942.5554 HBOND = 0.0000
1-4 VDW = 343.7922 1-4 EEL = -4216.3311 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1850 -1.5364E+05 1.8993E-01 9.3135E+00 H3' 1016
BOND = 10993.3161 ANGLE = 291.1858 DIHED = 881.8541
VDWAALS = 27303.2661 EEL = -189233.4068 HBOND = 0.0000
1-4 VDW = 343.6939 1-4 EEL = -4215.2406 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1900 -1.5379E+05 2.1217E-01 1.2168E+01 C2 818
BOND = 11026.9491 ANGLE = 290.8157 DIHED = 881.0640
VDWAALS = 27428.6766 EEL = -189550.6986 HBOND = 0.0000
1-4 VDW = 343.8640 1-4 EEL = -4213.9194 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1950 -1.5388E+05 2.4282E-01 1.1873E+01 O 9032
BOND = 11045.9685 ANGLE = 291.4548 DIHED = 880.3056
VDWAALS = 27487.4956 EEL = -189713.1037 HBOND = 0.0000
1-4 VDW = 343.6134 1-4 EEL = -4212.2553 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -1.5396E+05 2.1463E-01 1.0586E+01 C4' 996
BOND = 11052.7153 ANGLE = 290.9708 DIHED = 879.5720
VDWAALS = 27548.7108 EEL = -189861.5654 HBOND = 0.0000
1-4 VDW = 344.2268 1-4 EEL = -4210.3089 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2050 -1.5402E+05 2.7129E-01 1.4906E+01 O 9032
BOND = 11065.4560 ANGLE = 290.6544 DIHED = 879.7452
VDWAALS = 27589.7386 EEL = -189977.9115 HBOND = 0.0000
1-4 VDW = 344.2526 1-4 EEL = -4208.2635 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2100 -1.5409E+05 1.8151E-01 1.2188E+01 C2 818
BOND = 11073.7152 ANGLE = 289.4646 DIHED = 879.5329
VDWAALS = 27640.2499 EEL = -190108.6570 HBOND = 0.0000
1-4 VDW = 344.6921 1-4 EEL = -4207.5579 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2150 -1.5418E+05 1.3142E-01 5.5728E+00 Na+ 1349
BOND = 11090.4029 ANGLE = 289.3755 DIHED = 879.1518
VDWAALS = 27707.2482 EEL = -190285.3545 HBOND = 0.0000
1-4 VDW = 344.5387 1-4 EEL = -4206.9755 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2200 -1.5427E+05 1.2802E-01 5.8206E+00 P 1022
BOND = 11105.9511 ANGLE = 289.4093 DIHED = 878.9540
VDWAALS = 27769.2082 EEL = -190450.9691 HBOND = 0.0000
1-4 VDW = 344.4711 1-4 EEL = -4206.5323 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2250 -1.5434E+05 1.2233E-01 7.6481E+00 P 1022
BOND = 11118.3863 ANGLE = 289.5646 DIHED = 878.9649
VDWAALS = 27814.4284 EEL = -190584.3705 HBOND = 0.0000
1-4 VDW = 344.3955 1-4 EEL = -4206.2728 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2300 -1.5443E+05 1.0070E+00 6.7181E+01 H1 27579
BOND = 11145.6324 ANGLE = 293.2651 DIHED = 879.5173
VDWAALS = 27913.1397 EEL = -190801.3112 HBOND = 0.0000
1-4 VDW = 343.3844 1-4 EEL = -4204.8360 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2350 -1.5452E+05 4.1951E-01 2.0984E+01 O 27578
BOND = 11160.9940 ANGLE = 293.2938 DIHED = 879.0732
VDWAALS = 27970.8063 EEL = -190964.5029 HBOND = 0.0000
1-4 VDW = 342.9958 1-4 EEL = -4204.1858 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2400 -1.5460E+05 2.2246E-01 1.5291E+01 O 27608
BOND = 11172.7653 ANGLE = 290.0576 DIHED = 878.8340
VDWAALS = 28040.3481 EEL = -191123.9036 HBOND = 0.0000
1-4 VDW = 343.2092 1-4 EEL = -4204.2476 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2450 -1.5466E+05 2.3826E-01 1.1473E+01 P 1022
BOND = 11184.1558 ANGLE = 290.7913 DIHED = 878.7463
VDWAALS = 28077.3535 EEL = -191232.5490 HBOND = 0.0000
1-4 VDW = 343.3193 1-4 EEL = -4203.8372 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2500 -1.5472E+05 5.3890E-01 3.1856E+01 H1 26328
BOND = 11197.6011 ANGLE = 293.1576 DIHED = 878.3573
VDWAALS = 28137.6817 EEL = -191368.2955 HBOND = 0.0000
1-4 VDW = 343.3582 1-4 EEL = -4205.1036 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2500 -1.5472E+05 5.3890E-01 3.1856E+01 H1 26328
BOND = 11197.6011 ANGLE = 293.1576 DIHED = 878.3573
VDWAALS = 28137.6817 EEL = -191368.2955 HBOND = 0.0000
1-4 VDW = 343.3582 1-4 EEL = -4205.1036 RESTRAINT = 0.0000
"
Maybe my initial structure has serious problem. I found there are warning "---close contact---" when I check the input file in xleap. However, I build it as the tutorials and donot know how to deal witth it.
Regards,
Ouyang
----------------------------------------
> Date: Wed, 7 May 2008 08:57:03 -0700
> From: case.scripps.edu
> To: amber.scripps.edu
> Subject: Re: AMBER: Ewald error estimate
>
> On Wed, May 07, 2008, ???????????? wrote:
>>
>
>> I found a rather high van der Waals (VDWAALS and 1-4 VDW) energy although
>> after minimising the entire system.
>
> I don't see anything amiss in any of the results you posted. You need to be
> more specific about what you think the problem is. What do you think the vdW
> energies should be, and why?
>
> ....dac
>
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