Thanks for prompt reply Dr. David Case
If I put ntmin = 1, The steepest descent is proceed and conjugate gradient
stops and gives segmentation fault. So, I decided to carry out steepest
descent only. Then go to the next step heating the system and The namelist
was
&cntrl
imin = 0, nstlim = 500000, dt = 0.001,
ntb = 1, ntc = 2, ntf = 2,
irest = 0, ntx = 1,
tempi = 100.0, temp0 = 298.0,
ntt = 3, gamma_ln = 1.0, ig= -1,
ntr=1, restraintmask=':1-174', restraint_wt=20.0,
cut = 10.0, iwrap=1,
nmropt=1, ioutfm=1,
ntpr = 1000, ntwx = 1000, ntwr = 1000
/
&wt TYPE='TEMP0', istep1=0, istep2=500000,
value1=100.0, value2=298.0, /
&wt TYPE='END' /
However the output is very inconsistent (the temperature is very
flactuating), for example
vlimit exceeded for step 160005; vmax = 45.9534
vlimit exceeded for step 160006; vmax = 20.7918
vlimit exceeded for step 160094; vmax = 68.9744
vlimit exceeded for step 160097; vmax = 104.6940
vlimit exceeded for step 160141; vmax = 20.0547
vlimit exceeded for step 160142; vmax = 21.0159
vlimit exceeded for step 160156; vmax = 22.1678
vlimit exceeded for step 160160; vmax = 227.5223
vlimit exceeded for step 160181; vmax = 28.8740
vlimit exceeded for step 160182; vmax = 60.2265
vlimit exceeded for step 160183; vmax = 72.2278
vlimit exceeded for step 160191; vmax = 21.4153
vlimit exceeded for step 160192; vmax = 26.5000
vlimit exceeded for step 160195; vmax = 21.6114
vlimit exceeded for step 160196; vmax = 25.2856
vlimit exceeded for step 160249; vmax = 49.2674
vlimit exceeded for step 160261; vmax = 22.8969
vlimit exceeded for step 160262; vmax = 20.8973
vlimit exceeded for step 160293; vmax = 27.7145
vlimit exceeded for step 160294; vmax = 1636.2720
vlimit exceeded for step 160323; vmax = 23.9410
vlimit exceeded for step 160325; vmax = 185.4083
vlimit exceeded for step 160327; vmax = 33.5808
vlimit exceeded for step 160328; vmax = 53.1890
vlimit exceeded for step 160330; vmax = 136.6427
vlimit exceeded for step 160335; vmax = 23.6739
vlimit exceeded for step 160336; vmax = 22.6823
vlimit exceeded for step 160346; vmax = 20.0278
vlimit exceeded for step 160443; vmax = 30.7077
vlimit exceeded for step 160445; vmax = 52.6971
vlimit exceeded for step 160447; vmax = 845.9650
vlimit exceeded for step 160448; vmax = 27.5395
vlimit exceeded for step 160449; vmax = 38.5830
vlimit exceeded for step 160450; vmax = 132.0260
vlimit exceeded for step 160451; vmax = 23.1101
vlimit exceeded for step 160452; vmax = 25.3240
vlimit exceeded for step 160453; vmax = 31.9596
vlimit exceeded for step 160460; vmax = 20.6306
vlimit exceeded for step 160461; vmax = 24.0167
vlimit exceeded for step 160463; vmax = 20.6077
vlimit exceeded for step 160467; vmax = 20.2613
vlimit exceeded for step 160468; vmax = 20.1888
vlimit exceeded for step 160470; vmax = 21.2533
vlimit exceeded for step 160480; vmax = 22.1153
vlimit exceeded for step 160481; vmax = 24.1020
vlimit exceeded for step 160482; vmax = 20.0712
vlimit exceeded for step 160485; vmax = 26.4508
vlimit exceeded for step 160487; vmax = 22.1405
vlimit exceeded for step 160495; vmax = 20.9579
vlimit exceeded for step 160496; vmax = 21.8768
vlimit exceeded for step 160559; vmax = 23.0155
vlimit exceeded for step 160560; vmax = 39.3236
vlimit exceeded for step 160562; vmax = 26.9460
vlimit exceeded for step 160564; vmax = 55.9493
vlimit exceeded for step 160618; vmax = 23.4937
vlimit exceeded for step 160619; vmax = 20.5941
vlimit exceeded for step 160623; vmax = 38.1216
vlimit exceeded for step 160624; vmax = 22.5455
vlimit exceeded for step 160626; vmax = 28.8717
vlimit exceeded for step 160629; vmax = 90.5820
vlimit exceeded for step 160631; vmax = 98.0862
vlimit exceeded for step 160632; vmax = 24.5011
vlimit exceeded for step 160633; vmax = 20.5698
vlimit exceeded for step 160639; vmax = 20.0791
vlimit exceeded for step 160640; vmax = 20.5913
vlimit exceeded for step 160642; vmax = 26.5968
vlimit exceeded for step 160668; vmax = 20.9322
vlimit exceeded for step 160671; vmax = 22.1137
vlimit exceeded for step 160672; vmax = 22.0717
vlimit exceeded for step 160675; vmax = 31.4409
vlimit exceeded for step 160676; vmax = 54.6933
vlimit exceeded for step 160678; vmax = 21.3337
vlimit exceeded for step 160679; vmax = 20.1310
vlimit exceeded for step 160686; vmax = 21.3959
vlimit exceeded for step 160724; vmax = 20.0775
vlimit exceeded for step 160725; vmax = 20.5811
vlimit exceeded for step 160735; vmax = 20.7663
vlimit exceeded for step 160751; vmax = 20.2006
vlimit exceeded for step 160762; vmax = 35.0452
vlimit exceeded for step 160763; vmax = 121.5532
vlimit exceeded for step 160764; vmax = 22.2243
vlimit exceeded for step 160771; vmax = 24.1946
vlimit exceeded for step 160820; vmax = 49.7284
vlimit exceeded for step 160825; vmax = 20.1567
vlimit exceeded for step 160865; vmax = 35.8356
vlimit exceeded for step 160866; vmax = 38.5651
vlimit exceeded for step 160868; vmax = 39.9235
vlimit exceeded for step 160879; vmax = 22.1604
vlimit exceeded for step 160880; vmax = 22.6405
vlimit exceeded for step 160881; vmax = 106.2730
vlimit exceeded for step 160882; vmax = 27.4100
vlimit exceeded for step 160885; vmax = 22.9010
vlimit exceeded for step 160898; vmax = 25.9929
vlimit exceeded for step 160904; vmax = 41.5963
vlimit exceeded for step 160905; vmax = 21.1235
vlimit exceeded for step 160906; vmax = 82.4656
vlimit exceeded for step 160907; vmax = 21.6807
vlimit exceeded for step 160908; vmax = 26.0838
vlimit exceeded for step 160927; vmax = 20.5863
vlimit exceeded for step 160928; vmax = 21.9638
vlimit exceeded for step 160943; vmax = 20.2099
vlimit exceeded for step 160944; vmax = 21.1808
vlimit exceeded for step 160945; vmax = 23.9913
vlimit exceeded for step 160960; vmax = 23.0048
vlimit exceeded for step 160968; vmax = 20.0127
vlimit exceeded for step 160969; vmax = 21.4348
vlimit exceeded for step 160974; vmax = 20.2821
NSTEP = 161000 TIME(PS) = 161.000 TEMP(K) = 313.59 PRESS =
0.0
Etot = -84402.0287 EKtot = 20075.3127 EPtot =
-104477.3414
BOND = 2289.2463 ANGLE = 4077.3893 DIHED =
2531.9639
1-4 NB = 995.2811 1-4 EEL = 3723.7636 VDWAALS =
18000.0463
EELEC = -138176.2484 EHBOND = 0.0000 RESTRAINT =
2081.2165
EAMBER (non-restraint) = -106558.5580
Ewald error estimate: 0.9916E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 161002; vmax = 22.1030
vlimit exceeded for step 161006; vmax = 58.5121
vlimit exceeded for step 161008; vmax = 22.5513
vlimit exceeded for step 161010; vmax = 23.9847
vlimit exceeded for step 161011; vmax = 21.5275
vlimit exceeded for step 161037; vmax = 21.2026
vlimit exceeded for step 161083; vmax = 22.3301
vlimit exceeded for step 161084; vmax = 24.1807
vlimit exceeded for step 161089; vmax = 63.0853
vlimit exceeded for step 161090; vmax = 903.1390
vlimit exceeded for step 161091; vmax = 20.5449
vlimit exceeded for step 161156; vmax = 23.1385
vlimit exceeded for step 161160; vmax = 20.3862
vlimit exceeded for step 161164; vmax = 20.8849
vlimit exceeded for step 161181; vmax = 20.7049
vlimit exceeded for step 161185; vmax = 20.9107
vlimit exceeded for step 161186; vmax = 22.5145
vlimit exceeded for step 161226; vmax = 22.1239
vlimit exceeded for step 161227; vmax = 20.8822
vlimit exceeded for step 161242; vmax = 21.5333
vlimit exceeded for step 161318; vmax = 32.6290
vlimit exceeded for step 161320; vmax = 77.5207
vlimit exceeded for step 161324; vmax = 20.8543
vlimit exceeded for step 161327; vmax = 24.3299
vlimit exceeded for step 161329; vmax = 26.4359
vlimit exceeded for step 161373; vmax = 20.2981
vlimit exceeded for step 161374; vmax = 21.0344
vlimit exceeded for step 161446; vmax = 28.8446
vlimit exceeded for step 161447; vmax = 46.5560
vlimit exceeded for step 161448; vmax = 27.2647
vlimit exceeded for step 161454; vmax = 58.4400
vlimit exceeded for step 161455; vmax = 106.2411
vlimit exceeded for step 161456; vmax = 27.9814
vlimit exceeded for step 161463; vmax = 22.4622
vlimit exceeded for step 161464; vmax = 20.2181
vlimit exceeded for step 161474; vmax = 20.0476
vlimit exceeded for step 161477; vmax = 20.7897
vlimit exceeded for step 161491; vmax = 24.0602
vlimit exceeded for step 161507; vmax = 20.7244
vlimit exceeded for step 161512; vmax = 20.0074
vlimit exceeded for step 161527; vmax = 20.8875
vlimit exceeded for step 161546; vmax = 21.5552
vlimit exceeded for step 161547; vmax = 20.5946
vlimit exceeded for step 161553; vmax = 20.4414
vlimit exceeded for step 161554; vmax = 21.0824
vlimit exceeded for step 161562; vmax = 83.9855
vlimit exceeded for step 161612; vmax = 23.1177
vlimit exceeded for step 161613; vmax = 20.3653
vlimit exceeded for step 161617; vmax = 56.2864
vlimit exceeded for step 161619; vmax = 20.4698
vlimit exceeded for step 161639; vmax = 23.9027
vlimit exceeded for step 161667; vmax = 20.3998
vlimit exceeded for step 161668; vmax = 24.1470
vlimit exceeded for step 161786; vmax = 21.5114
vlimit exceeded for step 161791; vmax = 22.4662
vlimit exceeded for step 161795; vmax = 163.2657
vlimit exceeded for step 161804; vmax = 27.3528
vlimit exceeded for step 161851; vmax = 23.0340
vlimit exceeded for step 161861; vmax = 21.0584
vlimit exceeded for step 161900; vmax = 22.9455
vlimit exceeded for step 161901; vmax = 38.9883
vlimit exceeded for step 161903; vmax = 85.4033
vlimit exceeded for step 161905; vmax = 30.3493
vlimit exceeded for step 161906; vmax = 36.6068
vlimit exceeded for step 161960; vmax = 38.2209
vlimit exceeded for step 161964; vmax = 34.8292
vlimit exceeded for step 161966; vmax = 29.9031
vlimit exceeded for step 161967; vmax = 20.5596
vlimit exceeded for step 161970; vmax = 21.0092
vlimit exceeded for step 161982; vmax = 20.0092
vlimit exceeded for step 161983; vmax = 22.1871
NSTEP = 162000 TIME(PS) = 162.000 TEMP(K) = 260.12 PRESS =
0.0
Etot = -89034.3919 EKtot = 16652.3712 EPtot =
-105686.7632
BOND = 2078.7326 ANGLE = 3392.6927 DIHED =
2499.8736
1-4 NB = 918.3182 1-4 EEL = 3726.8583 VDWAALS =
17775.8004
EELEC = -138044.5859 EHBOND = 0.0000 RESTRAINT =
1965.5470
EAMBER (non-restraint) = -107652.3101
Ewald error estimate: 0.1054E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 162019; vmax = 23.6642
vlimit exceeded for step 162020; vmax = 26.1933
vlimit exceeded for step 162021; vmax = 93.0302
vlimit exceeded for step 162023; vmax = 309.3229
vlimit exceeded for step 162024; vmax = 28.5036
vlimit exceeded for step 162026; vmax = 26.5117
vlimit exceeded for step 162027; vmax = 20.2530
vlimit exceeded for step 162033; vmax = 21.5206
vlimit exceeded for step 162036; vmax = 21.0209
vlimit exceeded for step 162045; vmax = 20.2188
vlimit exceeded for step 162047; vmax = 21.6751
vlimit exceeded for step 162063; vmax = 31.5725
vlimit exceeded for step 162071; vmax = 20.4383
vlimit exceeded for step 162082; vmax = 23.3231
vlimit exceeded for step 162083; vmax = 21.0768
vlimit exceeded for step 162110; vmax = 20.6516
vlimit exceeded for step 162130; vmax = 20.0499
vlimit exceeded for step 162131; vmax = 21.2509
vlimit exceeded for step 162137; vmax = 20.8260
vlimit exceeded for step 162147; vmax = 26.4925
vlimit exceeded for step 162168; vmax = 23.4423
vlimit exceeded for step 162169; vmax = 34.8020
vlimit exceeded for step 162213; vmax = 22.6800
vlimit exceeded for step 162216; vmax = 41.4761
vlimit exceeded for step 162217; vmax = 30.3809
vlimit exceeded for step 162222; vmax = 57.1415
vlimit exceeded for step 162224; vmax = 38.5994
vlimit exceeded for step 162225; vmax = 20.2727
vlimit exceeded for step 162226; vmax = 30.2830
vlimit exceeded for step 162228; vmax = 82.3091
vlimit exceeded for step 162271; vmax = 21.9992
vlimit exceeded for step 162279; vmax = 32.0755
vlimit exceeded for step 162280; vmax = 170.2300
vlimit exceeded for step 162297; vmax = 1259.3006
vlimit exceeded for step 162298; vmax = 22.7251
vlimit exceeded for step 162299; vmax = 24.1811
vlimit exceeded for step 162301; vmax = 39.3719
vlimit exceeded for step 162302; vmax = 26.8566
vlimit exceeded for step 162304; vmax = 22.6915
vlimit exceeded for step 162306; vmax = 20.1735
vlimit exceeded for step 162307; vmax = 23.1690
vlimit exceeded for step 162309; vmax = 22.4974
vlimit exceeded for step 162327; vmax = 22.2416
vlimit exceeded for step 162328; vmax = 20.0262
vlimit exceeded for step 162352; vmax = 20.4401
vlimit exceeded for step 162399; vmax = 37.5554
vlimit exceeded for step 162422; vmax = 23.4048
vlimit exceeded for step 162423; vmax = 62.2173
vlimit exceeded for step 162424; vmax = 21.9311
vlimit exceeded for step 162429; vmax = 23.7378
vlimit exceeded for step 162430; vmax = 31.6054
vlimit exceeded for step 162431; vmax = 32.0804
vlimit exceeded for step 162437; vmax = 51.0472
vlimit exceeded for step 162440; vmax = 21.8037
vlimit exceeded for step 162441; vmax = 48.8020
vlimit exceeded for step 162442; vmax = 24.4937
vlimit exceeded for step 162448; vmax = 36.6093
vlimit exceeded for step 162449; vmax = 47.1057
vlimit exceeded for step 162453; vmax = 23.2547
vlimit exceeded for step 162454; vmax = 75.9150
vlimit exceeded for step 162461; vmax = 21.9564
vlimit exceeded for step 162463; vmax = 20.6729
vlimit exceeded for step 162464; vmax = 44.0916
vlimit exceeded for step 162465; vmax = 58.5036
vlimit exceeded for step 162473; vmax = 20.1925
vlimit exceeded for step 162474; vmax = 31.6944
vlimit exceeded for step 162475; vmax = 49.4007
vlimit exceeded for step 162477; vmax = 65.6641
vlimit exceeded for step 162485; vmax = 21.5343
vlimit exceeded for step 162489; vmax = 22.0471
vlimit exceeded for step 162490; vmax = 24.2094
vlimit exceeded for step 162510; vmax = 25.1482
vlimit exceeded for step 162511; vmax = 29.4826
vlimit exceeded for step 162512; vmax = 21.2926
vlimit exceeded for step 162572; vmax = 66.4651
vlimit exceeded for step 162573; vmax = 28.4668
vlimit exceeded for step 162575; vmax = 59.9446
vlimit exceeded for step 162576; vmax = 61.7363
vlimit exceeded for step 162577; vmax = 36.3646
vlimit exceeded for step 162617; vmax = 249.1811
vlimit exceeded for step 162618; vmax = 31.9960
vlimit exceeded for step 162631; vmax = 22.7700
vlimit exceeded for step 162633; vmax = 22.5380
vlimit exceeded for step 162653; vmax = 20.5019
vlimit exceeded for step 162654; vmax = 22.9463
vlimit exceeded for step 162656; vmax = 85.5694
vlimit exceeded for step 162657; vmax = 25.9675
vlimit exceeded for step 162664; vmax = 21.9963
vlimit exceeded for step 162672; vmax = 24.0380
vlimit exceeded for step 162673; vmax = 20.2387
vlimit exceeded for step 162679; vmax = 20.4935
vlimit exceeded for step 162680; vmax = 21.4441
vlimit exceeded for step 162697; vmax = 21.6463
vlimit exceeded for step 162698; vmax = 20.1133
vlimit exceeded for step 162699; vmax = 20.5499
vlimit exceeded for step 162707; vmax = 21.8196
vlimit exceeded for step 162708; vmax = 21.3608
vlimit exceeded for step 162715; vmax = 22.0411
vlimit exceeded for step 162716; vmax = 20.4748
vlimit exceeded for step 162722; vmax = 20.8935
vlimit exceeded for step 162723; vmax = 20.1305
vlimit exceeded for step 162724; vmax = 20.0134
vlimit exceeded for step 162751; vmax = 20.3428
vlimit exceeded for step 162763; vmax = 20.6775
vlimit exceeded for step 162770; vmax = 23.1789
vlimit exceeded for step 162797; vmax = 20.1014
vlimit exceeded for step 162801; vmax = 21.0077
vlimit exceeded for step 162805; vmax = 47.8679
vlimit exceeded for step 162807; vmax = 58.3906
vlimit exceeded for step 162979; vmax = 34.1244
vlimit exceeded for step 162991; vmax = 108.2562
vlimit exceeded for step 162992; vmax = 26.4714
NSTEP = 163000 TIME(PS) = 163.000 TEMP(K) = 303.60 PRESS =
0.0
Etot = -84044.9101 EKtot = 19436.0515 EPtot =
-103480.9616
BOND = 3144.3392 ANGLE = 3715.6143 DIHED =
2497.4785
1-4 NB = 1130.6357 1-4 EEL = 3730.6710 VDWAALS =
18186.3011
EELEC = -138401.9025 EHBOND = 0.0000 RESTRAINT =
2515.9011
EAMBER (non-restraint) = -105996.8628
Ewald error estimate: 0.3606E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
Thank you in advance for help
Said
On Tue, Oct 9, 2018 at 3:04 AM David Case <david.case.rutgers.edu> wrote:
> On Mon, Oct 08, 2018, Ibrahim Said wrote:
>
> > I built one of these carbon structures with hydroxyl groups and optimized
> > it with Gauss-16. I then used these structures as ligands for a protein.
> In
> > leap suite, I got only 22 warnings. When I saved both prmtop and inpcrd
> > files, I got the following message
> >
> > 1-4: angle 2862 2898 duplicates bond ('triangular' bond) or angle
> ('square'
> > bond)
>
> This should not be a problem, pre se. It means you have cyclopropane
> or cyclobutane like entities in your structure.
>
> > The problem is during minimization, steepest descent is only working and
>
> I think we'd have to know more about what is going on: why do you say
> that only steepest descent is working? It may be that you don't have a
> very well-minimized structure, but I have very little to go on.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 09 2018 - 04:00:02 PDT
