Date: Sat, 18 Jul 2020 02:09:30 -0500
Hi Amber Users,
I am trying to do steered molecular dynamics simulation between two
carbohydrates polymer to observe the shear phenomenon. There were two chain
parallel to each other. While I need to pull one chain towards a targeted
atom.
To do so, firstly, I have done the energy minimization with the following
input file given below:
Minimization with cartesian coordinates
&cntrl
imin=1, maxcyc=150000, ntmin=1,
ntb=1, ntc=1, ntf=1, irest=0, ntx=1,
tempi=298.0, temp0=298.0, dt=0.002, ig=-1,
ntr=1, restraintmask=':12-13', restraint_wt=10.0
ntwx=1000, ntpr=1000, ntwr=1000, ntxo=1, iwrap=1,
ioutfm=1,
/
And after that I have performed the steered molecular dynamics
simulation run using the file given below:
Sample pulling input
&cntrl
nstlim=150000, cut=10.0, igb=1, saltcon=0.1,
ntpr=100, ntwr=100000, ntt=1, ntb=1,
ntx=5, irest=1, ig=-1,
ntc=2, ntf=2, tol=0.000001,
dt=0.001, ntb=0, tempi=298.0, temp0=298.0,
ibelly=1,
bellymask=':1-2',
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist1.RST
DUMPAVE=dist1_vs_t
LISTIN=POUT
LISTOUT=POUT
And I am getting following error in the output file:
-------------------------------------------------------
Amber 18 SANDER 2018
-------------------------------------------------------
| Run on 07/17/2020 at 09:54:14
| Executable path: /home/sharmipc/amber18/bin/sander
| Working directory: /home/sharmipc/targetchain5/chain8
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: pulling.in
| MDOUT: pulling.out
|INPCRD: min4.rst7
| PARM: chain5.prmtop
|RESTRT: pulling.rst7
| REFC: min4.rst7
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: pulling.mdcrd
|MDINFO: pulling.info
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
Here is the input file:
Sample pulling input
&cntrl
nstlim=150000, cut=10.0, igb=1, saltcon=0.1,
ntpr=100, ntwr=100000, ntt=1, ntb=1,
ntx=5, irest=1, ig=-1,
ntc=2, ntf=2, tol=0.000001,
dt=0.001, ntb=0, tempi=298.0, temp0=298.0,
ibelly=1,
bellymask=':1-2',
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist1.RST
DUMPAVE=dist1_vs_t
LISTIN=POUT
LISTOUT=POUT
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 07/14/20 Time = 22:03:00
NATOM = 237 NTYPES = 6 NBONH = 114 MBONA = 131
NTHETH = 256 MTHETA = 193 NPHIH = 464 MPHIA = 378
NHPARM = 0 NPARM = 0 NNB = 1400 NRES = 13
NBONA = 131 NTHETA = 193 NPHIA = 378 NUMBND = 6
NUMANG = 14 NPTRA = 19 NATYP = 6 NPHB = 0
IFBOX = 1 NMXRS = 22 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 20389
| Hollerith 726
| Integer 32546
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 289 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
Note: ig = -1. Setting random seed to 997575 based on wallclock time in
microseconds.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 100, ntrx = 1, ntwr =
100000
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 0, igb = 1, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
Frozen or restrained atoms:
ibelly = 1, ntr = 0
Molecular dynamics:
nstlim = 150000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 298.00000, tempi = 298.00000, tautp = 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
LOADING THE BELLY ATOMS AS GROUPS
Mask :1-2; matches 23 atoms
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 7.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
DUMPFREQ 1 0 0.000000 0.000000 0 0
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = dist1.RST
DUMPAVE = dist1_vs_t
LISTIN = POUT
LISTOUT = POUT
Restraints will be read from file: dist1.RST
Here are comments from the DISANG input file:
jar option running
******
O1 ( 2)-O6 ( 225) NSTEP1= 0
NSTEP2=150000
R1 = -43.390 R2 = 56.610 R3 = 56.610 R4 = 156.610 RK2 = 10.000 RK3 =
10.000
R1A= -75.390 R2A= 24.610 R3A= 24.610 R4A= 124.610 RK2A= 10.000 RK3A=
10.000
Rcurr: 55.536 Rcurr-(R2+R3)/2: 1.074 MIN(Rcurr-R2,Rcurr-R3):
1.074
Number of restraints read = 1
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 58.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 58. NUM_NOSHAKE = 0 CORRECTED RNDFP = 58.
| TOTAL # of degrees of freedom (RNDF) = 58.
vlimit exceeded for step 0; vmax = 105.9069
vlimit exceeded for step 1; vmax = 20.0868
vlimit exceeded for step 2; vmax = 1695.5064
vlimit exceeded for step 3; vmax = 96.8094
vlimit exceeded for step 4; vmax = 24.6751
vlimit exceeded for step 5; vmax = 38.8814
vlimit exceeded for step 6; vmax = 32.3562
vlimit exceeded for step 7; vmax = 20.4149
vlimit exceeded for step 8; vmax = 21.9433
vlimit exceeded for step 9; vmax = 21.2149
vlimit exceeded for step 10; vmax = 20.5205
vlimit exceeded for step 11; vmax = 26.8177
vlimit exceeded for step 12; vmax = 29.8831
vlimit exceeded for step 13; vmax = 26.5275
vlimit exceeded for step 14; vmax = 20.9179
vlimit exceeded for step 15; vmax = 23.2847
vlimit exceeded for step 16; vmax = 22.5191
vlimit exceeded for step 17; vmax = 21.5735
vlimit exceeded for step 18; vmax = 20.3646
vlimit exceeded for step 19; vmax = 20.5492
vlimit exceeded for step 20; vmax = 23.1268
vlimit exceeded for step 21; vmax = 21.6957
vlimit exceeded for step 32; vmax = 35.3566
vlimit exceeded for step 33; vmax = 26.3343
vlimit exceeded for step 35; vmax = 117.6830
vlimit exceeded for step 36; vmax = 20.3232
vlimit exceeded for step 37; vmax = 26.1264
vlimit exceeded for step 38; vmax = 23.9091
vlimit exceeded for step 58; vmax = 26.1831
vlimit exceeded for step 59; vmax = 23.6240
vlimit exceeded for step 60; vmax = 22.1541
vlimit exceeded for step 62; vmax = 22.6694
vlimit exceeded for step 63; vmax = 22.2451
vlimit exceeded for step 71; vmax = 20.3256
vlimit exceeded for step 72; vmax = 432.5341
vlimit exceeded for step 73; vmax = 28.0919
vlimit exceeded for step 74; vmax = 32.3429
vlimit exceeded for step 75; vmax = 34.1458
vlimit exceeded for step 76; vmax = 20.5006
vlimit exceeded for step 77; vmax = 22.8381
vlimit exceeded for step 80; vmax = 21.9206
vlimit exceeded for step 81; vmax = 22.4076
vlimit exceeded for step 83; vmax = 36.4668
vlimit exceeded for step 84; vmax = 23.2616
vlimit exceeded for step 86; vmax = 24.4926
vlimit exceeded for step 87; vmax = 20.5590
vlimit exceeded for step 89; vmax = 25.3612
vlimit exceeded for step 90; vmax = 23.1876
vlimit exceeded for step 95; vmax = 27.3883
vlimit exceeded for step 96; vmax = 23.5077
vlimit exceeded for step 98; vmax = 21.7277
vlimit exceeded for step 99; vmax = 20.2530
NSTEP = 100 TIME(PS) = 7.100 TEMP(K) = 44477.33 PRESS =
0.0
Etot = 5487.3293 EKtot = 2563.1642 EPtot =
2924.1651
BOND = 1354.2670 ANGLE = 1297.7776 DIHED =
18.7441
1-4 NB = 88.9497 1-4 EEL = 119.5948 VDWAALS =
-1.8869
EELEC = -139.4685 EGB = 0.2582 RESTRAINT =
185.9291
EAMBER (non-restraint) = 2738.2360
------------------------------------------------------------------------------
NMR restraints: Bond = 185.929 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 103; vmax = 21.0856
vlimit exceeded for step 104; vmax = 53.8924
vlimit exceeded for step 106; vmax = 21.3814
vlimit exceeded for step 107; vmax = 20.9771
vlimit exceeded for step 108; vmax = 21.5204
vlimit exceeded for step 109; vmax = 21.3214
vlimit exceeded for step 112; vmax = 20.7206
vlimit exceeded for step 113; vmax = 117.0093
vlimit exceeded for step 114; vmax = 25.4293
vlimit exceeded for step 115; vmax = 33.6970
vlimit exceeded for step 116; vmax = 23.8302
vlimit exceeded for step 117; vmax = 22.3633
vlimit exceeded for step 121; vmax = 23.2351
vlimit exceeded for step 126; vmax = 22.5636
vlimit exceeded for step 127; vmax = 22.3797
vlimit exceeded for step 128; vmax = 21.7093
vlimit exceeded for step 131; vmax = 21.4934
vlimit exceeded for step 132; vmax = 21.3406
vlimit exceeded for step 135; vmax = 20.3570
vlimit exceeded for step 143; vmax = 21.5785
vlimit exceeded for step 144; vmax = 20.0872
vlimit exceeded for step 147; vmax = 26.0918
vlimit exceeded for step 148; vmax = 23.0709
vlimit exceeded for step 149; vmax = 20.0350
vlimit exceeded for step 153; vmax = 21.1516
vlimit exceeded for step 154; vmax = 20.0457
vlimit exceeded for step 155; vmax = 21.8696
vlimit exceeded for step 161; vmax = 21.6625
vlimit exceeded for step 162; vmax = 22.6948
vlimit exceeded for step 172; vmax = 47.6230
vlimit exceeded for step 173; vmax = 21.2281
vlimit exceeded for step 174; vmax = 22.0003
vlimit exceeded for step 177; vmax = 28.7469
vlimit exceeded for step 184; vmax = 21.0620
vlimit exceeded for step 185; vmax = 138.0760
vlimit exceeded for step 186; vmax = 56.6525
vlimit exceeded for step 187; vmax = 23.9787
vlimit exceeded for step 193; vmax = 20.1491
vlimit exceeded for step 194; vmax = 23.9393
vlimit exceeded for step 195; vmax = 20.0207
vlimit exceeded for step 198; vmax = 22.7723
NSTEP = 200 TIME(PS) = 7.200 TEMP(K) = 53478.72 PRESS =
0.0
Etot = 5299.5389 EKtot = 3081.9013 EPtot =
2217.6375
BOND = 1191.3758 ANGLE = 906.1134 DIHED =
14.6193
1-4 NB = 28.5941 1-4 EEL = 187.0657 VDWAALS =
-4.0667
EELEC = -105.0945 EGB = -28.4877 RESTRAINT =
27.5181
EAMBER (non-restraint) = 2190.1195
------------------------------------------------------------------------------
NMR restraints: Bond = 27.518 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 204; vmax = 27.6156
vlimit exceeded for step 206; vmax = 108.2871
vlimit exceeded for step 207; vmax = 21.9449
vlimit exceeded for step 208; vmax = 23.1374
vlimit exceeded for step 209; vmax = 25.3996
vlimit exceeded for step 210; vmax = 23.1810
vlimit exceeded for step 211; vmax = 36.9165
vlimit exceeded for step 215; vmax = 20.3443
vlimit exceeded for step 216; vmax = 38.1515
vlimit exceeded for step 217; vmax = 21.1317
vlimit exceeded for step 218; vmax = 20.9519
vlimit exceeded for step 222; vmax = 132.7577
vlimit exceeded for step 223; vmax = 29.1874
vlimit exceeded for step 226; vmax = 22.5218
vlimit exceeded for step 227; vmax = 21.3648
vlimit exceeded for step 228; vmax = 21.0264
vlimit exceeded for step 229; vmax = 25.7850
vlimit exceeded for step 232; vmax = 22.0910
vlimit exceeded for step 233; vmax = 47.6627
vlimit exceeded for step 236; vmax = 22.4632
vlimit exceeded for step 237; vmax = 22.0506
vlimit exceeded for step 239; vmax = 20.7257
vlimit exceeded for step 240; vmax = 21.2316
vlimit exceeded for step 243; vmax = 32.2029
vlimit exceeded for step 245; vmax = 24.1875
vlimit exceeded for step 246; vmax = 20.5713
vlimit exceeded for step 249; vmax = 41.0676
vlimit exceeded for step 250; vmax = 24.6342
vlimit exceeded for step 251; vmax = 29.5716
vlimit exceeded for step 253; vmax = 21.2033
vlimit exceeded for step 254; vmax = 20.3749
vlimit exceeded for step 255; vmax = 32.0916
vlimit exceeded for step 264; vmax = 20.2020
vlimit exceeded for step 265; vmax = 20.5443
vlimit exceeded for step 266; vmax = 21.7443
vlimit exceeded for step 268; vmax = 20.1010
vlimit exceeded for step 269; vmax = 23.0592
vlimit exceeded for step 280; vmax = 30.8850
vlimit exceeded for step 281; vmax = 77.0654
vlimit exceeded for step 282; vmax = 21.0398
vlimit exceeded for step 287; vmax = 22.5738
vlimit exceeded for step 288; vmax = 27.6498
vlimit exceeded for step 291; vmax = 22.2659
vlimit exceeded for step 292; vmax = 29.1865
vlimit exceeded for step 295; vmax = 21.7720
NSTEP = 300 TIME(PS) = 7.300 TEMP(K) = 46733.11 PRESS =
0.0
Etot = 4858.9377 EKtot = 2693.1620 EPtot =
2165.7756
BOND = 1010.8114 ANGLE = 822.5539 DIHED =
22.0839
1-4 NB = 99.6949 1-4 EEL = 159.2130 VDWAALS =
152.5415
EELEC = -61.2007 EGB = -52.0338 RESTRAINT =
12.1116
EAMBER (non-restraint) = 2153.6641
------------------------------------------------------------------------------
NMR restraints: Bond = 12.112 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 305; vmax = 20.1330
vlimit exceeded for step 306; vmax = 22.4699
vlimit exceeded for step 310; vmax = 20.6531
vlimit exceeded for step 329; vmax = 21.6199
vlimit exceeded for step 330; vmax = 71.0083
vlimit exceeded for step 331; vmax = 23.9040
vlimit exceeded for step 332; vmax = 20.0357
vlimit exceeded for step 333; vmax = 24.5861
vlimit exceeded for step 334; vmax = 21.0286
vlimit exceeded for step 335; vmax = 26.6698
vlimit exceeded for step 336; vmax = 20.2135
vlimit exceeded for step 354; vmax = 20.7841
vlimit exceeded for step 379; vmax = 25.9944
vlimit exceeded for step 380; vmax = 29.5294
vlimit exceeded for step 381; vmax = 115.2994
vlimit exceeded for step 382; vmax = 21.7681
vlimit exceeded for step 383; vmax = 24.0199
vlimit exceeded for step 384; vmax = 22.7652
vlimit exceeded for step 385; vmax = 21.9065
vlimit exceeded for step 386; vmax = 21.8418
vlimit exceeded for step 389; vmax = 35.9228
vlimit exceeded for step 392; vmax = 81.9062
vlimit exceeded for step 393; vmax = 23.3766
vlimit exceeded for step 394; vmax = 155.2352
vlimit exceeded for step 395; vmax = 26.0166
vlimit exceeded for step 396; vmax = 20.3037
vlimit exceeded for step 397; vmax = 22.5333
NSTEP = 400 TIME(PS) = 7.400 TEMP(K) = 56185.88 PRESS =
0.0
Etot = 4974.3558 EKtot = 3237.9112 EPtot =
1736.4446
BOND = 847.3888 ANGLE = 728.1392 DIHED =
14.1284
1-4 NB = 51.0781 1-4 EEL = 252.1886 VDWAALS =
-5.0681
EELEC = -189.0630 EGB = 37.4787 RESTRAINT =
0.1739
EAMBER (non-restraint) = 1736.2708
------------------------------------------------------------------------------
NMR restraints: Bond = 0.174 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 401; vmax = 22.0233
vlimit exceeded for step 402; vmax = 23.1909
vlimit exceeded for step 419; vmax = 20.1087
vlimit exceeded for step 420; vmax = 20.2737
vlimit exceeded for step 427; vmax = 20.5742
vlimit exceeded for step 428; vmax = 22.9416
vlimit exceeded for step 429; vmax = 25.9005
vlimit exceeded for step 433; vmax = 21.7064
vlimit exceeded for step 434; vmax = 26.1840
vlimit exceeded for step 435; vmax = 22.0085
vlimit exceeded for step 436; vmax = 22.1269
vlimit exceeded for step 439; vmax = 22.0977
vlimit exceeded for step 442; vmax = 985.8633
vlimit exceeded for step 443; vmax = 27.3088
vlimit exceeded for step 444; vmax = 111.4868
vlimit exceeded for step 445; vmax = 168.1922
vlimit exceeded for step 446; vmax = 20.5438
vlimit exceeded for step 448; vmax = 21.8158
vlimit exceeded for step 449; vmax = 20.0664
vlimit exceeded for step 451; vmax = 38.8839
vlimit exceeded for step 452; vmax = 21.5626
vlimit exceeded for step 453; vmax = 25.6785
vlimit exceeded for step 454; vmax = 25.0394
vlimit exceeded for step 455; vmax = 26.1935
vlimit exceeded for step 456; vmax = 21.6698
vlimit exceeded for step 457; vmax = 20.7136
vlimit exceeded for step 458; vmax = 21.1151
vlimit exceeded for step 460; vmax = 22.7944
vlimit exceeded for step 462; vmax = 112.4568
vlimit exceeded for step 463; vmax = 25.2298
vlimit exceeded for step 465; vmax = 21.9399
vlimit exceeded for step 466; vmax = 21.8509
vlimit exceeded for step 467; vmax = 24.2068
vlimit exceeded for step 468; vmax = 24.3925
vlimit exceeded for step 469; vmax = 21.9787
vlimit exceeded for step 470; vmax = 21.9658
vlimit exceeded for step 471; vmax = 21.9217
vlimit exceeded for step 472; vmax = 21.9600
vlimit exceeded for step 473; vmax = 22.4993
vlimit exceeded for step 474; vmax = 22.8303
vlimit exceeded for step 475; vmax = 23.9798
vlimit exceeded for step 476; vmax = 24.4384
vlimit exceeded for step 477; vmax = 24.0651
vlimit exceeded for step 478; vmax = 23.1662
vlimit exceeded for step 479; vmax = 22.2049
vlimit exceeded for step 480; vmax = 21.9664
vlimit exceeded for step 481; vmax = 24.3487
vlimit exceeded for step 482; vmax = 25.5125
vlimit exceeded for step 483; vmax = 24.0904
vlimit exceeded for step 484; vmax = 21.8005
vlimit exceeded for step 485; vmax = 21.6866
vlimit exceeded for step 486; vmax = 21.9314
vlimit exceeded for step 487; vmax = 22.2325
vlimit exceeded for step 488; vmax = 22.4958
vlimit exceeded for step 489; vmax = 22.6413
vlimit exceeded for step 490; vmax = 22.5915
vlimit exceeded for step 491; vmax = 22.3070
vlimit exceeded for step 492; vmax = 21.8432
vlimit exceeded for step 493; vmax = 22.1980
vlimit exceeded for step 494; vmax = 22.3449
vlimit exceeded for step 495; vmax = 23.7409
vlimit exceeded for step 496; vmax = 22.8229
vlimit exceeded for step 497; vmax = 22.1709
vlimit exceeded for step 498; vmax = 20.8216
vlimit exceeded for step 499; vmax = 39.4030
NSTEP = 500 TIME(PS) = 7.500 TEMP(K) =710444.91 PRESS =
0.0
Etot = 86352.7572 EKtot = 40941.9160 EPtot =
45410.8412
BOND = 42989.9353 ANGLE = 1390.1842 DIHED =
19.6264
1-4 NB = 354.3866 1-4 EEL = 168.5414 VDWAALS =
1.2608
EELEC = -101.0915 EGB = -63.6559 RESTRAINT =
651.6539
EAMBER (non-restraint) = 44759.1873
------------------------------------------------------------------------------
NMR restraints: Bond = 651.654 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 500; vmax = 20.9246
vlimit exceeded for step 501; vmax = 20.8824
vlimit exceeded for step 502; vmax = 20.7764
vlimit exceeded for step 503; vmax = 20.9610
vlimit exceeded for step 504; vmax = 21.4823
vlimit exceeded for step 505; vmax = 21.7814
vlimit exceeded for step 506; vmax = 21.7317
vlimit exceeded for step 507; vmax = 23.9249
vlimit exceeded for step 508; vmax = 22.2453
vlimit exceeded for step 509; vmax = 42.9417
vlimit exceeded for step 510; vmax = 20.8366
vlimit exceeded for step 513; vmax = 21.9027
vlimit exceeded for step 514; vmax = 22.4552
vlimit exceeded for step 515; vmax = 23.7240
vlimit exceeded for step 516; vmax = 22.6261
vlimit exceeded for step 517; vmax = 21.0917
vlimit exceeded for step 518; vmax = 20.0843
vlimit exceeded for step 521; vmax = 20.3488
vlimit exceeded for step 522; vmax = 20.5448
vlimit exceeded for step 525; vmax = 22.9417
vlimit exceeded for step 526; vmax = 22.8099
vlimit exceeded for step 527; vmax = 20.7190
vlimit exceeded for step 528; vmax = 23.1560
vlimit exceeded for step 529; vmax = 22.5486
vlimit exceeded for step 535; vmax = 43.6703
vlimit exceeded for step 536; vmax = 26.2744
vlimit exceeded for step 538; vmax = 51.9193
vlimit exceeded for step 539; vmax = 22.4573
vlimit exceeded for step 540; vmax = 26.7623
vlimit exceeded for step 541; vmax = 20.2678
vlimit exceeded for step 542; vmax = 30.6914
vlimit exceeded for step 543; vmax = 23.0495
vlimit exceeded for step 544; vmax = 21.1774
vlimit exceeded for step 546; vmax = 23.6157
vlimit exceeded for step 547; vmax = 29.3612
vlimit exceeded for step 548; vmax = 26.1123
vlimit exceeded for step 549; vmax = 26.3516
vlimit exceeded for step 550; vmax = 26.3234
vlimit exceeded for step 551; vmax = 22.6417
vlimit exceeded for step 552; vmax = 21.3671
vlimit exceeded for step 553; vmax = 21.0663
vlimit exceeded for step 554; vmax = 25.4519
vlimit exceeded for step 555; vmax = 24.7839
vlimit exceeded for step 556; vmax = 22.3196
vlimit exceeded for step 557; vmax = 21.3011
vlimit exceeded for step 558; vmax = 22.7111
vlimit exceeded for step 559; vmax = 22.4751
vlimit exceeded for step 560; vmax = 22.2129
vlimit exceeded for step 561; vmax = 24.9753
vlimit exceeded for step 562; vmax = 23.4306
vlimit exceeded for step 563; vmax = 23.3539
vlimit exceeded for step 564; vmax = 22.2880
vlimit exceeded for step 565; vmax = 21.5293
vlimit exceeded for step 566; vmax = 23.0636
vlimit exceeded for step 567; vmax = 23.4453
vlimit exceeded for step 568; vmax = 22.8513
vlimit exceeded for step 569; vmax = 23.2262
vlimit exceeded for step 570; vmax = 24.0931
vlimit exceeded for step 571; vmax = 22.6130
vlimit exceeded for step 572; vmax = 23.9307
vlimit exceeded for step 573; vmax = 23.0851
vlimit exceeded for step 574; vmax = 22.2588
vlimit exceeded for step 575; vmax = 21.9060
vlimit exceeded for step 576; vmax = 23.2759
vlimit exceeded for step 577; vmax = 24.2566
vlimit exceeded for step 578; vmax = 22.7697
vlimit exceeded for step 579; vmax = 25.3894
vlimit exceeded for step 580; vmax = 26.5380
vlimit exceeded for step 581; vmax = 23.4732
vlimit exceeded for step 582; vmax = 24.2905
vlimit exceeded for step 583; vmax = 25.5110
vlimit exceeded for step 584; vmax = 25.9952
vlimit exceeded for step 585; vmax = 24.8091
vlimit exceeded for step 586; vmax = 21.8046
vlimit exceeded for step 587; vmax = 22.1280
vlimit exceeded for step 588; vmax = 21.1586
vlimit exceeded for step 589; vmax = 23.1670
vlimit exceeded for step 590; vmax = 24.8234
vlimit exceeded for step 591; vmax = 23.7939
vlimit exceeded for step 592; vmax = 27.0881
vlimit exceeded for step 593; vmax = 25.8332
vlimit exceeded for step 594; vmax = 23.0350
vlimit exceeded for step 595; vmax = 22.0383
vlimit exceeded for step 596; vmax = 21.7001
vlimit exceeded for step 597; vmax = 23.7975
vlimit exceeded for step 598; vmax = 21.5144
vlimit exceeded for step 599; vmax = 21.3758
NSTEP = 600 TIME(PS) = 7.600 TEMP(K) =********* PRESS =
0.0
Etot = 63560.6907 EKtot = 61828.4949 EPtot =
1732.1958
BOND = 883.4374 ANGLE = 619.6759 DIHED =
19.9304
1-4 NB = 74.2947 1-4 EEL = 191.6657 VDWAALS =
40.3739
EELEC = -153.4317 EGB = 8.3085 RESTRAINT =
47.9411
EAMBER (non-restraint) = 1684.2547
------------------------------------------------------------------------------
NMR restraints: Bond = 47.941 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 600; vmax = 21.2876
vlimit exceeded for step 601; vmax = 21.9011
vlimit exceeded for step 602; vmax = 23.8600
vlimit exceeded for step 603; vmax = 22.7445
vlimit exceeded for step 604; vmax = 21.5671
vlimit exceeded for step 605; vmax = 21.4715
vlimit exceeded for step 606; vmax = 21.4383
vlimit exceeded for step 607; vmax = 409.6201
vlimit exceeded for step 608; vmax = 8123.4138
vlimit exceeded for step 609; vmax = 252.1823
vlimit exceeded for step 610; vmax = 68.7057
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 7 11 12
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
And when I have used this input file of pulling,
Sample pulling input
&cntrl
nstlim=500000, cut=10.0, igb=0, saltcon=0.1,
ntpr=100, ntt=3, gamma_ln=1.0,
ntx=5, irest=1, ntwx=1000, ig = 256251,
ntc=2, ntf=2, tol=0.000001,
dt=0.001, ntb=0,
tempi=300.0, temp0=300.0,
ibelly=1,
bellymask= ':1-2',
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist1.RST
DUMPAVE=dist1_vs_t
LISTIN=POUT
LISTOUT=POUT
I have got the following error :
*Error: I could not find enough velocities in the min.rst7 file.* ( which
is the restrt file I have found after energy minimization. ( the image of
output file attached herewith.)
In this point, I am wondering that have I save the incprd file correctly
from the xleap. There were 237 atoms in the pdb file but I have found less
number of atoms in the mdcrd /rstrt file. Please find the rst7 file given
below and also tell me the meaning of the last three columns.
defa
237
11.4478405 16.5000041 47.7254919 10.5580416 16.0984837 47.6979278
10.4601647 15.1886363 48.7896837 9.5813126 14.5580672 48.6487754
11.6639354 14.3551690 48.8065467 11.6559279 13.3187996 49.8758688
10.7494620 12.7192847 49.7648356 12.8696863 12.3901533 49.6903687
13.7912869 12.9501585 49.8295535 12.8510430 11.5764722 50.4157638
12.8523783 11.8362507 48.3626511 12.5767870 12.5245559 47.7476297
11.6343521 14.0043661 51.2559576 12.5882736 14.5107204 51.4004879
10.4800679 15.0448223 51.3604283 9.5422663 14.4984013 51.4759498
10.6525786 15.9165686 52.5199159 9.8816784 16.5065326 52.5207414
10.3673122 15.9737687 50.1247157 11.1808409 16.7008196 50.1557213
9.1029026 16.6956582 50.1980279 8.9704127 17.1609660 49.3607119
11.4915641 12.9005592 52.2425719 12.0796059 13.1215878 53.5681569
12.9416704 13.7759461 53.4628965 11.0822807 13.7736862 54.4165523
11.5069718 14.0678579 55.8006216 12.4514506 14.6132114 55.7779453
10.4463512 14.9841651 56.4324893 9.4946434 14.4581488 56.5149496
10.7526332 15.3060467 57.4281790 10.2741068 16.1395629 55.5902732
10.3126582 15.8333882 54.6713759 11.7367872 12.7298372 56.5162621
10.7974880 12.1738259 56.5442288 12.8098326 11.9075221 55.7416035
13.7752733 12.3902586 55.8779288 12.9071153 10.5631287 56.2855697
13.5358803 10.5537327 57.0288461 12.5335976 11.7845243 54.2138323
11.7551297 11.0377653 54.0474207 13.7603890 11.3406945 53.5640868
13.9945248 10.4821515 53.9404306 12.1350955 13.0781512 57.9062309
12.2708503 11.9956591 58.8815004 11.5786565 11.1884176 58.6363295
13.6495137 11.5024219 58.8393656 13.9459506 10.3804422 59.7680216
13.2309748 9.5783262 59.5726527 15.3611785 9.8355833 59.4754463
16.1143880 10.5500556 59.7987828 15.5295538 8.9027050 60.0137845
15.5172574 9.6002828 58.0585565 16.4180416 9.8366215 57.7803997
13.7522811 10.8855750 61.2138516 14.5045995 11.6466685 61.4084868
12.3339806 11.5062874 61.3952630 11.6018203 10.6971245 61.3719924
12.2065379 12.2044666 62.6684249 11.2832078 12.5001359 62.7113310
11.9781813 12.5401834 60.2975959 12.5723069 13.4419611 60.4547348
10.5695822 12.8969071 60.4184597 10.3755571 13.6219149 59.8115288
13.9896905 9.7213878 62.1056075 14.4089332 10.0094392 63.4864760
14.9227429 10.9707038 63.5139489 13.2188796 10.0744062 64.3420016
13.4626102 10.3526907 65.7745698 14.0321097 11.2773407 65.8589471
12.1025700 10.5780421 66.4511483 11.4713641 9.6951974 66.3444421
12.2257226 10.7923805 67.5130807 11.4671752 11.6992578 65.8147663
11.5648200 11.5797200 64.8598026 14.2945271 9.2094157 66.3744837
13.6952762 8.2963978 66.3619679 15.5932859 9.0005271 65.5461437
16.2679389 9.8342151 65.7481343 16.2430642 7.7699769 65.9560412
16.6017894 7.8655423 66.8577069 15.3548392 8.8997120 64.0135457
14.9069367 7.9308681 63.7844921 16.6430673 8.9865031 63.3386361
17.1958122 8.2813867 63.7036930 14.5788924 9.6019617 67.7841221
14.9329504 8.5230337 68.7228756 14.3697686 7.6238629 68.4674728
16.3740608 8.2447411 68.6263902 16.9002216 7.1679015 69.5170535
16.3898628 6.2402564 69.2499821 18.4177638 6.9627581 69.3010259
18.9893432 7.7083106 69.8529005 18.7088729 5.9796269 69.6717764
18.7701476 7.0594563 67.9074237 18.8553727 8.0039075 67.6775565
16.5713247 7.5296110 70.9819355 17.1772522 8.3854665 71.2852911
16.9047522 6.4008229 71.8252336 16.6156065 6.6160846 72.7221485
15.0731111 7.8756699 71.1686343 14.4765855 6.9728961 71.0216887
14.8647981 8.3477928 72.5286999 13.9425076 8.6255820 72.6038243
14.5969985 8.9577204 70.1720398 15.0969344 9.9023354 70.3910568
13.1574612 9.1491034 70.3178935 12.8819222 9.9070038 69.7900142
14.4690340 16.0023886 44.8632508 13.9915141 16.5023777 45.5281231
14.1609616 15.7837764 46.7396807 13.3520297 15.0602443 46.8460975
15.4338594 15.0760308 46.6127924 15.7990030 14.2221120 47.7736230
15.0149195 13.4738659 47.8989618 17.1234773 13.4972047 47.4652344
17.9208043 14.2230833 47.3014448 17.4116224 12.8551940 48.2981400
16.9795698 12.6868956 46.2870365 16.6282322 13.2352864 45.5787274
15.8958119 15.0670864 49.0618025 16.8117886 15.6604235 49.0225963
14.6803833 16.0252643 49.2399875 13.8448950 15.4434133 49.6279001
15.0090108 17.0611744 50.2083418 14.5634222 16.8663462 51.0547498
14.2202582 16.7507092 47.9524301 14.9272004 17.5494789 47.7184564
12.9128176 17.3506407 48.2135629 13.0716901 18.1049695 48.7984107
16.0062140 14.0689999 50.1681100 16.2170193 14.5480437 51.5397114
16.9613226 15.3461504 51.5329850 14.9504802 15.0385084 52.0822002
15.0901313 15.7087209 53.3962185 15.8785035 16.4600857 53.3127955
13.7802421 16.4474882 53.7486045 13.0430539 15.7458041 54.1245059
13.9600300 17.1922386 54.5241031 13.2196814 17.0921979 52.5853920
12.2648732 16.9054023 52.5985201 15.5134400 14.6425924 54.4278585
14.6832659 13.9496622 54.5563676 16.7632555 13.8382080 53.9383432
17.6442800 14.4709393 54.0589435 16.9597979 12.6195422 54.7152194
17.6389048 12.1171680 54.2408173 16.6719091 13.3883344 52.4534236
15.9423064 12.5809739 52.3677670 17.9685110 12.8776166 52.0228482
17.8784631 12.5171417 51.1319466 15.7337104 15.3775633 55.7038453
15.6037855 14.5775608 56.9282630 14.8319549 13.8248938 56.7788572
16.8797314 13.9118458 57.1861522 16.8243076 12.9663968 58.3078114
15.9337382 12.3462553 58.1994254 18.0450482 12.0414614 58.2119304
18.9558699 12.6149819 58.0365742 18.1720265 11.4601973 59.1251278
17.8170383 11.1364491 57.1148546 17.5452144 11.6747381 56.3482267
16.6721186 13.7994133 59.5838219 17.5226480 14.4779927 59.6767408
15.3452316 14.6065618 59.4833392 14.5184551 13.8986518 59.5234930
15.2196988 15.5044140 60.6193627 15.0214373 14.9914354 61.4201276
15.2218141 15.4344712 58.1670967 15.8846528 16.2999930 58.2157221
13.8472540 15.8987601 58.0320473 13.6626807 16.4897987 58.7724912
16.6876765 12.8357446 60.7111153 16.8525697 13.3719177 62.0638229
17.3670006 14.3335220 62.0234999 15.5223139 13.5428910 62.6573239
15.4993668 14.0708971 64.0475747 15.9754066 15.0534205 64.0333558
14.0437100 14.2484728 64.5386166 13.6444327 13.3007545 64.8984056
14.0165999 14.9601436 65.3641204 13.1903956 14.7187164 63.4831007
12.8711270 13.9298265 63.0168276 16.2971918 13.1349763 64.9810534
15.7316854 12.2124450 65.1022261 17.6993090 12.7718805 64.4035880
18.3585220 13.6332650 64.5241919 18.2796445 11.6358686 65.1057679
19.1083490 11.4268246 64.6509952 17.6609675 12.3682645 62.9103324
17.1886459 11.3918205 62.8155752 19.0263199 12.2691919 62.4061576
19.0217229 11.7635096 61.5851208 16.3756281 13.8514729 66.2876931
16.2628727 13.0254081 67.5004354 15.4102086 12.3495342 67.4066072
17.4921956 12.2543957 67.6532355 17.5685481 11.3471170 68.8134230
16.7250661 10.6629845 68.7714715 18.8811174 10.5560804 68.7274528
19.7314020 11.2382074 68.7634798 18.9607372 9.8666229 69.5667701
18.9151277 9.8172296 67.4884939 18.7167046 10.4490608 66.7755509
17.4648267 12.1940308 70.0836022 18.3530086 12.8232438 70.1664983
17.4028456 11.2972149 71.2182237 17.2662247 11.8407988 72.0059475
16.1964244 13.0802016 70.0515461 15.3161099 12.4386670 70.1314258
16.2299836 13.9639637 71.2043724 15.4705194 14.5578741 71.1447633
16.0852852 13.9225562 68.7543658 16.8601219 14.6913992 68.7542397
14.7791680 14.5699872 68.7266131 14.7182328 15.1302282 67.9441205
13.8803839 12.0433664 -11.3821638 14.0724576 11.0553976 -10.9642795
13.9192937 13.0688053 -10.3067635 15.2543344 13.3059409 -9.7096925
15.5783992 12.3762465 -9.2389302 15.1011772 14.3916563 -8.6316554
14.8012404 15.3341876 -9.0921403 16.0427897 14.5440068 -8.1069231
14.0886834 13.9950481 -7.6857757 13.2914408 13.7698364 -8.1766697
16.2580368 13.6902339 -10.8140345 15.9968502 14.6706282 -11.2174640
16.2778755 12.6567521 -11.9671549 16.7083993 11.7233983 -11.5976835
17.1011462 13.1527195 -13.0567886 17.1642849 12.4678386 -13.7318719
14.8626122 12.3732087 -12.5245807 14.5040841 13.2477866 -13.0712911
14.9223416 11.2391465 -13.4407307 14.0952453 11.1342037 -13.9231727
17.5861574 13.7675127 -10.1857277
30.6200000 26.0960000 105.8020000 90.0000000 90.0000000 90.0000000
Any help would be highly appreciated.
-- Pinky, Sharmi AL,US
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(image/png attachment: pull.png)
