it's not just that the energy is positive, it is that the initial bond
energy is EXTREMELY large.
Minimization may have fixed it, but I would look at the structure very
carefully to make sure it is sensible.
Bad things can happen when energies are so high (such as chirality
inversions and more).
The angle energy and 1-4 EEL still seem quite large, that is probably why
your total energy is positive.
On Sat, Dec 12, 2020 at 3:06 PM Pinky Mazumder <pmazumder67.gmail.com>
wrote:
> Thank you so much for your valuable suggestions.
>
> Another issue when I am performing the energy minimization, the value of
> energy is positive. But, I am expecting some negative value. I am doing
> energy minimization in order to relax the structure. The output is given
> below:
>
>
> Please help me to solve this issue.
>
> -------------------------------------------------------
> Amber 18 SANDER 2018
> -------------------------------------------------------
>
> | Run on 12/12/2020 at 05:36:19
>
> | Executable path: /home/smazumder/amber18/bin/sander
> | Working directory: /home/smazumder/Documents/charge
> | Hostname: Unknown
> [-O]verwriting output
>
> File Assignments:
> | MDIN: min.mdin
>
> | MDOUT: min.mdout
>
> |INPCRD: c.inpcrd
>
> | PARM: c.prmtop
>
> |RESTRT: min.inpcrd
>
> | REFC: refc
>
> | MDVEL: mdvel
>
> | MDFRC: mdfrc
>
> | MDEN: mden
>
> | MDCRD: mdcrd
>
> |MDINFO: mdinfo
>
> | MTMD: mtmd
>
> |INPDIP: inpdip
>
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
>
>
>
> Here is the input file:
>
> polyA-polyT 10-mer: initial minimisation prior to MD
>
> &cntrl
>
> imin = 1,
>
> maxcyc = 5000,
>
> ncyc = 2500,
>
> ntb = 0,
>
> igb = 0,
>
> cut = 12
>
> /
>
>
>
>
>
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags:
>
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> |Largest sphere to fit in unit cell has radius = 41.349
> | New format PARM file being parsed.
> | Version = 1.000 Date = 12/12/20 Time = 03:10:03
> NATOM = 8400 NTYPES = 10 NBONH = 4000 MBONA = 4800
> NTHETH = 9200 MTHETA = 7200 NPHIH = 20000 MPHIA = 19200
> NHPARM = 0 NPARM = 0 NNB = 50800 NRES = 400
> NBONA = 4800 NTHETA = 7200 NPHIA = 19200 NUMBND = 15
> NUMANG = 32 NPTRA = 83 NATYP = 1 NPHB = 0
> IFBOX = 0 NMXRS = 21 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Force field information read from topology file:
> | CHARMM: >>>>>>>>>>>> All-hydrogen parameters used in the
> <<<<<<<<<<<<<<<<
> |
> |CHARMM: CHARMM force field in use.
> |CHARMM: Overriding default value of chngmask.
> |CHARMM: Setting chngmask = 0.
>
> | Memory Use Allocated
> | Real 662667
> | Hollerith 25602
> | Integer 2118105
> | Max Pairs 4838400
> | nblistReal 100800
> | nblist Int 2258336
> | Total 42060 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
>
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
>
>
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
> 1
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0
> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 1, ntb = 0, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 5000, ncyc = 2500, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
> | INFO: Old style inpcrd file read
>
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = -0.00000000
> Forcing neutrality...
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 2306055
> | TOTAL SIZE OF NONBOND LIST = 2306055
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 3.5109E+07 2.0077E+03 3.5690E+04 C1 6490
>
> BOND = 35045114.0805 ANGLE = 9080.9995 DIHED =
> 13519.9019
> UB = 1460.4671 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = -2919.4190 EEL = -13625.7824 HBOND =
> 0.0000
> 1-4 VDW = 2148.8221 1-4 EEL = 54238.1182 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 2.2898E+07 8.5421E+03 7.0458E+05 C1 3760
>
> BOND = 22580665.4767 ANGLE = 50752.1199 DIHED =
> 13821.6427
> UB = 11107.6592 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 192113.0374 EEL = -12027.7632 HBOND =
> 0.0000
> 1-4 VDW = 7994.9176 1-4 EEL = 53463.1130 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 1.2117E+07 1.1500E+03 8.9731E+04 O2 3620
>
> BOND = 11787956.3477 ANGLE = 83692.5272 DIHED =
> 13760.3208
> UB = 68858.8991 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 83155.4910 EEL = -8655.5713 HBOND =
> 0.0000
> 1-4 VDW = 34700.7548 1-4 EEL = 53785.4664 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 150 7.6843E+06 3.3907E+02 2.4018E+04 O4 4846
>
> BOND = 7299558.1066 ANGLE = 119890.6314 DIHED =
> 13567.9299
> UB = 119728.3630 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 72004.0285 EEL = -11754.6198 HBOND =
> 0.0000
> 1-4 VDW = 17641.2461 1-4 EEL = 53712.5814 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 5.5288E+06 1.2210E+02 2.7747E+03 H1 4181
>
> BOND = 5062951.9509 ANGLE = 148524.8410 DIHED =
> 13431.8779
> UB = 191301.7328 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 52713.2322 EEL = -17316.2481 HBOND =
> 0.0000
> 1-4 VDW = 23935.0405 1-4 EEL = 53235.8871 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 250 4.0306E+06 5.0353E+03 4.5552E+05 O4 4174
>
> BOND = 3487274.9810 ANGLE = 171994.6999 DIHED =
> 13915.3139
> UB = 205442.0102 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 95401.1675 EEL = -17346.5290 HBOND =
> 0.0000
> 1-4 VDW = 21651.5222 1-4 EEL = 52313.5232 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 300 3.0016E+06 6.3307E+01 1.4003E+03 C1 4810
>
> BOND = 2551403.8145 ANGLE = 175326.0092 DIHED =
> 13860.2844
> UB = 164486.8064 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 52492.0157 EEL = -23753.7061 HBOND =
> 0.0000
> 1-4 VDW = 15537.3735 1-4 EEL = 52268.2912 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 350 3.9631E+06 1.8876E+05 1.2988E+07 C1 4600
>
> BOND = 1989541.0080 ANGLE = 175630.1150 DIHED =
> 13700.3422
> UB = 130955.6173 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1610754.3207 EEL = -29330.9715 HBOND =
> 0.0000
> 1-4 VDW = 19098.1053 1-4 EEL = 52723.0168 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 400 1.9888E+06 8.0647E+03 7.2014E+05 O3 4905
>
> BOND = 1505874.2324 ANGLE = 171420.4032 DIHED =
> 13663.2521
> UB = 100814.8458 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 160175.4301 EEL = -29674.9822 HBOND =
> 0.0000
> 1-4 VDW = 13362.4692 1-4 EEL = 53211.8761 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 450 1.4918E+06 1.0109E+03 1.0344E+05 C3 4840
>
> BOND = 1158306.4669 ANGLE = 159167.3693 DIHED =
> 13878.3041
> UB = 76784.7978 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 43366.8040 EEL = -35799.7110 HBOND =
> 0.0000
> 1-4 VDW = 22700.9637 1-4 EEL = 53361.2302 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 1.3185E+06 4.9488E+01 3.2985E+03 C1 4852
>
> BOND = 1011379.4002 ANGLE = 152663.0017 DIHED =
> 13984.4165
> UB = 67671.9685 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 41264.5009 EEL = -34208.7229 HBOND =
> 0.0000
> 1-4 VDW = 12281.7696 1-4 EEL = 53427.7126 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 550 1.1439E+06 6.9149E+01 6.2101E+03 C5 4623
>
> BOND = 854394.5903 ANGLE = 145412.7598 DIHED =
> 14027.8973
> UB = 57774.1299 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 39492.3681 EEL = -33409.1809 HBOND =
> 0.0000
> 1-4 VDW = 12579.6245 1-4 EEL = 53644.5203 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 600 9.4450E+05 1.2874E+02 1.2097E+04 O5 4625
>
> BOND = 673198.0998 ANGLE = 137711.5543 DIHED =
> 13955.9660
> UB = 45809.3430 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 39443.4772 EEL = -31904.3455 HBOND =
> 0.0000
> 1-4 VDW = 12134.7494 1-4 EEL = 54150.2891 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 650 7.5857E+05 3.9470E+01 1.9696E+03 H4 4824
>
> BOND = 513808.0677 ANGLE = 128458.3015 DIHED =
> 13953.2789
> UB = 33566.1653 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 34159.1276 EEL = -31665.7913 HBOND =
> 0.0000
> 1-4 VDW = 11720.5819 1-4 EEL = 54573.1524 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 700 6.0110E+05 3.3884E+01 3.5579E+03 O4 4846
>
> BOND = 386621.6657 ANGLE = 113468.7848 DIHED =
> 13916.7633
> UB = 24173.7005 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 31639.6857 EEL = -34454.9090 HBOND =
> 0.0000
> 1-4 VDW = 10954.0897 1-4 EEL = 54784.7270 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 750 4.8452E+05 1.9104E+01 1.0857E+03 C1 2080
>
> BOND = 291784.6024 ANGLE = 100394.4341 DIHED =
> 13917.1108
> UB = 18327.3883 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 29571.5200 EEL = -34602.9304 HBOND =
> 0.0000
> 1-4 VDW = 10194.1224 1-4 EEL = 54928.8510 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 800 4.1220E+05 1.3144E+01 4.7606E+02 O4 1066
>
> BOND = 233204.7830 ANGLE = 92096.2365 DIHED =
> 13928.8842
> UB = 14781.9368 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 28149.8832 EEL = -34924.0989 HBOND =
> 0.0000
> 1-4 VDW = 9891.5212 1-4 EEL = 55074.2202 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 850 3.5894E+05 1.8068E+01 1.9463E+03 C1 5440
>
> BOND = 193546.1302 ANGLE = 85060.5024 DIHED =
> 13913.2619
> UB = 12337.2463 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 27120.3334 EEL = -37734.9057 HBOND =
> 0.0000
> 1-4 VDW = 9604.0635 1-4 EEL = 55089.8061 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 900 3.1316E+05 9.8434E+00 6.0403E+02 C1 5440
>
> BOND = 157712.3937 ANGLE = 79126.9914 DIHED =
> 13924.6168
> UB = 10396.0207 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 25819.1829 EEL = -38306.5974 HBOND =
> 0.0000
> 1-4 VDW = 9354.2536 1-4 EEL = 55128.8400 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 950 2.7846E+05 1.7978E+01 1.3904E+03 C1 5860
>
> BOND = 132678.5148 ANGLE = 73492.4255 DIHED =
> 13985.1688
> UB = 8875.3830 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 23546.2842 EEL = -38489.1476 HBOND =
> 0.0000
> 1-4 VDW = 9209.1830 1-4 EEL = 55166.6484 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1000 2.5323E+05 1.1635E+01 8.4480E+02 C1 5860
>
> BOND = 112069.1740 ANGLE = 68760.1224 DIHED =
> 14004.0358
> UB = 7834.2304 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 22593.0367 EEL = -36130.8007 HBOND =
> 0.0000
> 1-4 VDW = 8935.1908 1-4 EEL = 55166.9860 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1050 2.3268E+05 1.5114E+01 1.0500E+03 C1 5440
>
> BOND = 99046.8994 ANGLE = 64575.9520 DIHED =
> 13975.9794
> UB = 7041.3437 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 20528.7624 EEL = -36256.4461 HBOND =
> 0.0000
> 1-4 VDW = 8572.7328 1-4 EEL = 55197.9156 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1100 2.1518E+05 1.1672E+01 8.7582E+02 C1 5440
>
> BOND = 86124.3447 ANGLE = 61029.3303 DIHED =
> 13942.9903
> UB = 6359.8293 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 20064.1336 EEL = -35742.3424 HBOND =
> 0.0000
> 1-4 VDW = 8167.3326 1-4 EEL = 55234.4626 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1150 2.0205E+05 1.3150E+01 1.1195E+03 C1 5440
>
> BOND = 77459.6886 ANGLE = 57434.9257 DIHED =
> 13934.0246
> UB = 5805.2594 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 18787.7572 EEL = -34461.9743 HBOND =
> 0.0000
> 1-4 VDW = 7798.7232 1-4 EEL = 55292.8361 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1200 1.8977E+05 1.0335E+01 7.3444E+02 O4 5266
>
> BOND = 68553.0991 ANGLE = 54242.8964 DIHED =
> 13920.6893
> UB = 5305.2274 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 18358.8056 EEL = -33465.0872 HBOND =
> 0.0000
> 1-4 VDW = 7500.9009 1-4 EEL = 55353.5198 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1250 1.7821E+05 1.1404E+01 8.9761E+02 C1 5440
>
> BOND = 62464.8476 ANGLE = 51350.4331 DIHED =
> 13908.9998
> UB = 4921.1221 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 17159.6306 EEL = -34252.9535 HBOND =
> 0.0000
> 1-4 VDW = 7247.4193 1-4 EEL = 55408.3837 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1300 1.6653E+05 6.6808E+00 4.7703E+02 O4 2326
>
> BOND = 55533.3490 ANGLE = 48662.5993 DIHED =
> 13898.2965
> UB = 4533.4976 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 16601.0217 EEL = -35149.0531 HBOND =
> 0.0000
> 1-4 VDW = 7000.9979 1-4 EEL = 55445.7528 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1350 1.5742E+05 8.9883E+00 6.3028E+02 C1 2500
>
> BOND = 50849.0895 ANGLE = 46024.0528 DIHED =
> 13916.2446
> UB = 4205.7861 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 15548.5009 EEL = -35341.0762 HBOND =
> 0.0000
> 1-4 VDW = 6761.7146 1-4 EEL = 55456.3043 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1400 1.4834E+05 5.0438E+00 3.1976E+02 O4 5266
>
> BOND = 45966.0812 ANGLE = 43621.0572 DIHED =
> 13949.8455
> UB = 3892.2597 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 14901.0228 EEL = -35960.1837 HBOND =
> 0.0000
> 1-4 VDW = 6521.6528 1-4 EEL = 55446.3677 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1450 1.4212E+05 8.3414E+00 6.0410E+02 O4 5266
>
> BOND = 42453.3492 ANGLE = 41286.0950 DIHED =
> 13980.1014
> UB = 3632.4745 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 14153.8672 EEL = -35102.9370 HBOND =
> 0.0000
> 1-4 VDW = 6291.2019 1-4 EEL = 55421.7812 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1500 1.3602E+05 4.9563E+00 3.9677E+02 O4 5266
>
> BOND = 38620.7124 ANGLE = 39240.7253 DIHED =
> 13999.4266
> UB = 3383.3428 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 13764.7120 EEL = -34457.5419 HBOND =
> 0.0000
> 1-4 VDW = 6078.9516 1-4 EEL = 55386.6732 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1550 1.3128E+05 7.3340E+00 5.5411E+02 O4 5266
>
> BOND = 35989.6227 ANGLE = 37268.2337 DIHED =
> 14017.0099
> UB = 3181.4423 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 12980.6410 EEL = -33377.4237 HBOND =
> 0.0000
> 1-4 VDW = 5866.3250 1-4 EEL = 55356.1922 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1600 1.2613E+05 4.1941E+00 3.1928E+02 O4 5266
>
> BOND = 32924.8447 ANGLE = 35434.3161 DIHED =
> 14024.7920
> UB = 2984.7022 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 12661.7329 EEL = -32901.4117 HBOND =
> 0.0000
> 1-4 VDW = 5671.8372 1-4 EEL = 55327.3960 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1650 1.2079E+05 9.5723E+00 9.5761E+02 O4 5266
>
> BOND = 30461.7416 ANGLE = 33625.7007 DIHED =
> 14021.3216
> UB = 2817.9449 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 12317.3113 EEL = -33241.3433 HBOND =
> 0.0000
> 1-4 VDW = 5490.1918 1-4 EEL = 55301.4723 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1700 1.1529E+05 3.3643E+00 1.7818E+02 O4 7366
>
> BOND = 28412.5477 ANGLE = 31985.8810 DIHED =
> 14026.9304
> UB = 2672.4569 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 11540.5943 EEL = -33954.8315 HBOND =
> 0.0000
> 1-4 VDW = 5312.9971 1-4 EEL = 55289.8440 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1750 1.1110E+05 6.1795E+00 5.8091E+02 O4 3166
>
> BOND = 26367.5304 ANGLE = 30476.8901 DIHED =
> 14039.4398
> UB = 2532.7733 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 11177.2101 EEL = -33927.4968 HBOND =
> 0.0000
> 1-4 VDW = 5149.6659 1-4 EEL = 55288.7107 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1800 1.0699E+05 7.0649E+00 5.2718E+02 O4 3166
>
> BOND = 24963.6112 ANGLE = 28962.3992 DIHED =
> 14052.2806
> UB = 2413.7128 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 10512.5399 EEL = -34204.4773 HBOND =
> 0.0000
> 1-4 VDW = 4993.9671 1-4 EEL = 55292.9291 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1850 1.0377E+05 4.4007E+00 3.5998E+02 O4 5266
>
> BOND = 23073.1797 ANGLE = 27592.7874 DIHED =
> 14054.6091
> UB = 2286.1650 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 10185.4674 EEL = -33561.3588 HBOND =
> 0.0000
> 1-4 VDW = 4838.8297 1-4 EEL = 55300.4411 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1900 1.0117E+05 5.6889E+00 5.0969E+02 O4 5266
>
> BOND = 21749.1509 ANGLE = 26359.8842 DIHED =
> 14057.9878
> UB = 2182.8486 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 9757.0458 EEL = -32945.7262 HBOND =
> 0.0000
> 1-4 VDW = 4693.2573 1-4 EEL = 55314.2250 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1950 9.9204E+04 4.0654E+00 3.0468E+02 O4 5266
>
> BOND = 20174.6734 ANGLE = 25189.8797 DIHED =
> 14061.6952
> UB = 2074.3397 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 9532.7066 EEL = -31698.3893 HBOND =
> 0.0000
> 1-4 VDW = 4544.5718 1-4 EEL = 55324.5990 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2000 9.6628E+04 5.0073E+00 3.9172E+02 O4 5266
>
> BOND = 19286.1388 ANGLE = 24119.4714 DIHED =
> 14070.9971
> UB = 1993.4415 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 9024.1624 EEL = -31620.5460 HBOND =
> 0.0000
> 1-4 VDW = 4415.4567 1-4 EEL = 55338.6522 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2050 9.4596E+04 6.7424E+00 5.6536E+02 O4 5266
>
> BOND = 18427.9255 ANGLE = 23062.7739 DIHED =
> 14082.1147
> UB = 1911.2834 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 8617.6365 EEL = -31151.2157 HBOND =
> 0.0000
> 1-4 VDW = 4290.2637 1-4 EEL = 55355.0949 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2100 9.2404E+04 4.9026E+00 4.1327E+02 C2 5361
>
> BOND = 17402.8591 ANGLE = 22085.9759 DIHED =
> 14096.9321
> UB = 1830.1678 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 8350.2190 EEL = -30914.2780 HBOND =
> 0.0000
> 1-4 VDW = 4185.5058 1-4 EEL = 55366.6527 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2150 9.0590E+04 6.6631E+00 5.0322E+02 C2 5361
>
> BOND = 16778.1586 ANGLE = 21210.0141 DIHED =
> 14108.9993
> UB = 1765.2755 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 8013.3939 EEL = -30763.1264 HBOND =
> 0.0000
> 1-4 VDW = 4100.8324 1-4 EEL = 55376.7754 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2200 8.8403E+04 4.2653E+00 3.6243E+02 C2 5361
>
> BOND = 15905.1447 ANGLE = 20394.4207 DIHED =
> 14112.8433
> UB = 1700.0393 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 7816.1079 EEL = -30932.2880 HBOND =
> 0.0000
> 1-4 VDW = 4021.9520 1-4 EEL = 55385.1846 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2250 8.5961E+04 2.0569E+00 1.2098E+02 O4 5266
>
> BOND = 15168.5936 ANGLE = 19664.7633 DIHED =
> 14114.5536
> UB = 1639.7575 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 7593.9584 EEL = -31565.8219 HBOND =
> 0.0000
> 1-4 VDW = 3949.1118 1-4 EEL = 55396.4298 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2300 8.4292E+04 3.6117E+00 2.4943E+02 O4 5266
>
> BOND = 14664.1280 ANGLE = 18982.8243 DIHED =
> 14117.5218
> UB = 1589.5634 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 7329.6476 EEL = -31676.3250 HBOND =
> 0.0000
> 1-4 VDW = 3879.0020 1-4 EEL = 55406.0904 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2350 8.2733E+04 4.9048E+00 3.3708E+02 O4 5266
>
> BOND = 14251.2226 ANGLE = 18341.7086 DIHED =
> 14115.7752
> UB = 1544.8212 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 7070.2323 EEL = -31812.6682 HBOND =
> 0.0000
> 1-4 VDW = 3811.1490 1-4 EEL = 55410.6534 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2400 8.0699E+04 3.3971E+00 2.6793E+02 O4 5266
>
> BOND = 13574.6814 ANGLE = 17789.5579 DIHED =
> 14112.9227
> UB = 1493.6979 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 7014.7442 EEL = -32450.7480 HBOND =
> 0.0000
> 1-4 VDW = 3747.8101 1-4 EEL = 55416.0369 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2450 7.8697E+04 1.6428E+00 8.1024E+01 O4 5266
>
> BOND = 13227.8842 ANGLE = 17216.9028 DIHED =
> 14107.7472
> UB = 1453.9320 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 6754.8177 EEL = -33173.2152 HBOND =
> 0.0000
> 1-4 VDW = 3686.3842 1-4 EEL = 55422.3632 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2500 7.7646E+04 2.8307E+00 2.3404E+02 O4 3166
>
> BOND = 12892.2950 ANGLE = 16720.2064 DIHED =
> 14097.5105
> UB = 1416.3566 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 6551.4452 EEL = -33094.2069 HBOND =
> 0.0000
> 1-4 VDW = 3632.3202 1-4 EEL = 55429.7190 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2550 6.8670E+04 4.5242E+00 3.0439E+02 C2 3261
>
> BOND = 10344.7312 ANGLE = 13578.4466 DIHED =
> 14019.7638
> UB = 1209.4277 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 5343.9773 EEL = -34713.6525 HBOND =
> 0.0000
> 1-4 VDW = 3341.4205 1-4 EEL = 55546.2140 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2600 6.5775E+04 4.5751E+00 1.8628E+02 O4 5266
>
> BOND = 9757.9853 ANGLE = 12525.4002 DIHED =
> 13973.2571
> UB = 1134.5822 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 4934.2051 EEL = -35292.5915 HBOND =
> 0.0000
> 1-4 VDW = 3186.4220 1-4 EEL = 55555.8688 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2650 6.3908E+04 3.3797E+00 1.2129E+02 C1 5440
>
> BOND = 9324.9529 ANGLE = 11698.5336 DIHED =
> 13945.3697
> UB = 1072.1058 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 4559.8023 EEL = -35342.8938 HBOND =
> 0.0000
> 1-4 VDW = 3074.0398 1-4 EEL = 55576.4857 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2700 6.3675E+04 3.2699E+00 1.4955E+02 C1 5440
>
> BOND = 8964.5327 ANGLE = 11006.1713 DIHED =
> 13919.0714
> UB = 1023.5512 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 4272.6610 EEL = -34071.8122 HBOND =
> 0.0000
> 1-4 VDW = 2966.5612 1-4 EEL = 55593.9990 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2750 6.2594E+04 3.0464E+00 1.1124E+02 C2 5361
>
> BOND = 8702.6782 ANGLE = 10329.7897 DIHED =
> 13886.2867
> UB = 986.7514 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 3953.9780 EEL = -33757.4093 HBOND =
> 0.0000
> 1-4 VDW = 2882.4587 1-4 EEL = 55609.4810 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2800 6.1393E+04 2.9241E+00 1.1159E+02 C1 5440
>
> BOND = 8410.2794 ANGLE = 9827.9731 DIHED =
> 13859.4435
> UB = 954.6775 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 3721.0894 EEL = -33810.3727 HBOND =
> 0.0000
> 1-4 VDW = 2813.1400 1-4 EEL = 55616.8267 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2850 6.0255E+04 2.9189E+00 1.0820E+02 C1 5440
>
> BOND = 8202.4833 ANGLE = 9381.6191 DIHED =
> 13832.9300
> UB = 925.9202 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 3502.6107 EEL = -33969.6960 HBOND =
> 0.0000
> 1-4 VDW = 2754.6762 1-4 EEL = 55624.6914 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2900 5.8978E+04 2.6326E+00 1.0068E+02 O4 5266
>
> BOND = 8034.7211 ANGLE = 8995.3582 DIHED =
> 13796.6103
> UB = 896.8702 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 3292.3663 EEL = -34383.6533 HBOND =
> 0.0000
> 1-4 VDW = 2706.1500 1-4 EEL = 55639.4023 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2950 5.7632E+04 2.6530E+00 8.1753E+01 C1 5440
>
> BOND = 7873.5896 ANGLE = 8650.9133 DIHED =
> 13765.4187
> UB = 873.8612 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 3138.7588 EEL = -34992.3509 HBOND =
> 0.0000
> 1-4 VDW = 2666.1335 1-4 EEL = 55656.0918 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3000 5.6327E+04 2.5647E+00 8.6747E+01 C1 5440
>
> BOND = 7751.3606 ANGLE = 8354.1316 DIHED =
> 13744.2781
> UB = 854.7280 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2963.8693 EEL = -35632.1096 HBOND =
> 0.0000
> 1-4 VDW = 2628.3244 1-4 EEL = 55662.6550 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3050 5.5787E+04 2.4284E+00 8.6479E+01 O4 5266
>
> BOND = 7646.9921 ANGLE = 8091.1408 DIHED =
> 13726.6144
> UB = 836.5749 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2818.2467 EEL = -35598.6542 HBOND =
> 0.0000
> 1-4 VDW = 2593.7352 1-4 EEL = 55671.9042 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3100 5.5251E+04 2.2049E+00 7.0304E+01 C1 5440
>
> BOND = 7540.2663 ANGLE = 7858.5807 DIHED =
> 13705.6591
> UB = 820.2886 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2693.1560 EEL = -35609.8540 HBOND =
> 0.0000
> 1-4 VDW = 2567.2395 1-4 EEL = 55675.7837 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3150 5.4761E+04 2.1122E+00 6.2083E+01 C3 5785
>
> BOND = 7474.9277 ANGLE = 7658.0808 DIHED =
> 13683.8919
> UB = 807.4659 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2572.3335 EEL = -35658.9033 HBOND =
> 0.0000
> 1-4 VDW = 2542.9510 1-4 EEL = 55680.2458 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3200 5.4255E+04 2.1327E+00 5.8130E+01 C3 5785
>
> BOND = 7403.6182 ANGLE = 7479.2157 DIHED =
> 13660.5632
> UB = 794.9271 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2489.3260 EEL = -35775.3256 HBOND =
> 0.0000
> 1-4 VDW = 2516.6477 1-4 EEL = 55685.5941 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3250 5.4093E+04 2.1447E+00 6.0960E+01 O4 3166
>
> BOND = 7335.5199 ANGLE = 7302.7091 DIHED =
> 13633.1746
> UB = 783.5040 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2414.3444 EEL = -35566.9238 HBOND =
> 0.0000
> 1-4 VDW = 2495.6468 1-4 EEL = 55695.2049 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3300 5.4701E+04 2.2130E+00 7.5425E+01 O4 3166
>
> BOND = 7280.5049 ANGLE = 7138.5414 DIHED =
> 13614.2690
> UB = 771.4349 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2326.0034 EEL = -34608.3526 HBOND =
> 0.0000
> 1-4 VDW = 2473.8387 1-4 EEL = 55705.1517 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3350 5.4637E+04 2.3162E+00 1.0030E+02 O4 3166
>
> BOND = 7230.8224 ANGLE = 6983.0260 DIHED =
> 13598.4211
> UB = 757.4913 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2229.8960 EEL = -34327.3566 HBOND =
> 0.0000
> 1-4 VDW = 2447.6926 1-4 EEL = 55716.8311 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3400 5.5054E+04 1.9339E+00 7.1069E+01 O4 3166
>
> BOND = 7184.2605 ANGLE = 6838.0073 DIHED =
> 13589.2648
> UB = 746.3675 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2145.1846 EEL = -33597.6525 HBOND =
> 0.0000
> 1-4 VDW = 2422.9899 1-4 EEL = 55725.6883 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3450 5.4859E+04 1.8487E+00 6.7365E+01 O4 5266
>
> BOND = 7137.4900 ANGLE = 6704.1458 DIHED =
> 13579.3438
> UB = 736.4658 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2085.0606 EEL = -33524.5040 HBOND =
> 0.0000
> 1-4 VDW = 2401.7604 1-4 EEL = 55739.4443 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3500 5.4447E+04 1.7723E+00 7.1475E+01 O4 5266
>
> BOND = 7098.2062 ANGLE = 6587.0723 DIHED =
> 13568.7690
> UB = 728.9187 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 2023.7898 EEL = -33688.0900 HBOND =
> 0.0000
> 1-4 VDW = 2381.1673 1-4 EEL = 55747.0144 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3550 5.4200E+04 1.6709E+00 6.8513E+01 O4 5266
>
> BOND = 7063.9265 ANGLE = 6484.8605 DIHED =
> 13558.7845
> UB = 721.9156 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1963.4065 EEL = -33714.5720 HBOND =
> 0.0000
> 1-4 VDW = 2364.0988 1-4 EEL = 55757.6184 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3600 5.3651E+04 1.5873E+00 5.5609E+01 O4 5266
>
> BOND = 7022.7948 ANGLE = 6393.3004 DIHED =
> 13550.7161
> UB = 714.5703 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1919.9686 EEL = -34065.7840 HBOND =
> 0.0000
> 1-4 VDW = 2348.0646 1-4 EEL = 55767.2204 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3650 5.3554E+04 1.4908E+00 5.7097E+01 O4 5266
>
> BOND = 6987.6337 ANGLE = 6307.5379 DIHED =
> 13545.2436
> UB = 707.4025 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1878.2732 EEL = -33978.3638 HBOND =
> 0.0000
> 1-4 VDW = 2333.3159 1-4 EEL = 55773.1051 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3700 5.3677E+04 1.3623E+00 4.7442E+01 O4 5266
>
> BOND = 6958.5120 ANGLE = 6225.5124 DIHED =
> 13540.4668
> UB = 701.4490 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1836.6265 EEL = -33682.9671 HBOND =
> 0.0000
> 1-4 VDW = 2320.6825 1-4 EEL = 55776.5001 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3750 5.3599E+04 1.2932E+00 4.2510E+01 O4 5266
>
> BOND = 6932.3875 ANGLE = 6148.1616 DIHED =
> 13535.4452
> UB = 695.9467 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1795.2862 EEL = -33599.7656 HBOND =
> 0.0000
> 1-4 VDW = 2309.3633 1-4 EEL = 55781.9478 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3800 5.3063E+04 1.2137E+00 3.8727E+01 O4 5266
>
> BOND = 6899.3401 ANGLE = 6076.7483 DIHED =
> 13529.0438
> UB = 691.0534 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1759.1037 EEL = -33978.0862 HBOND =
> 0.0000
> 1-4 VDW = 2298.9551 1-4 EEL = 55786.5536 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3850 5.3079E+04 1.0349E+00 2.5938E+01 O4 7366
>
> BOND = 6860.6789 ANGLE = 6002.1602 DIHED =
> 13525.3887
> UB = 686.4824 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1731.4740 EEL = -33801.2987 HBOND =
> 0.0000
> 1-4 VDW = 2287.4468 1-4 EEL = 55786.5539 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3900 5.2719E+04 1.0052E+00 2.8278E+01 O4 5686
>
> BOND = 6837.0612 ANGLE = 5915.2415 DIHED =
> 13518.3000
> UB = 681.0713 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1685.1303 EEL = -33982.0205 HBOND =
> 0.0000
> 1-4 VDW = 2274.9950 1-4 EEL = 55789.4293 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3950 5.2452E+04 1.0196E+00 3.4162E+01 O4 5686
>
> BOND = 6802.4801 ANGLE = 5838.9708 DIHED =
> 13511.6009
> UB = 676.0229 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1647.1300 EEL = -34080.5165 HBOND =
> 0.0000
> 1-4 VDW = 2263.2080 1-4 EEL = 55792.7518 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4000 5.2423E+04 1.0478E+00 2.8400E+01 C5 5778
>
> BOND = 6812.5385 ANGLE = 5767.3741 DIHED =
> 13505.6291
> UB = 673.7939 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1578.5682 EEL = -33956.4378 HBOND =
> 0.0000
> 1-4 VDW = 2251.3521 1-4 EEL = 55790.3267 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4050 5.2770E+04 9.7253E-01 2.0584E+01 C5 5778
>
> BOND = 6769.9611 ANGLE = 5706.8407 DIHED =
> 13501.1449
> UB = 669.2987 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1564.9777 EEL = -33476.8598 HBOND =
> 0.0000
> 1-4 VDW = 2241.8710 1-4 EEL = 55792.9956 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4100 5.2370E+04 1.3088E+00 4.5738E+01 O4 5266
>
> BOND = 6755.0920 ANGLE = 5643.3555 DIHED =
> 13493.7258
> UB = 666.5770 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1523.3892 EEL = -33733.7702 HBOND =
> 0.0000
> 1-4 VDW = 2230.8691 1-4 EEL = 55791.1903 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4150 5.2384E+04 9.2345E-01 3.1374E+01 C1 5860
>
> BOND = 6739.9862 ANGLE = 5586.7842 DIHED =
> 13487.0632
> UB = 662.6404 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1497.3034 EEL = -33592.2907 HBOND =
> 0.0000
> 1-4 VDW = 2219.9401 1-4 EEL = 55782.4582 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4200 5.2361E+04 8.7189E-01 2.9230E+01 C1 5860
>
> BOND = 6728.2109 ANGLE = 5539.4359 DIHED =
> 13481.0854
> UB = 660.2480 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1473.1361 EEL = -33506.6056 HBOND =
> 0.0000
> 1-4 VDW = 2210.3391 1-4 EEL = 55775.5666 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4250 5.2040E+04 9.5748E-01 2.1652E+01 C5 5778
>
> BOND = 6719.7802 ANGLE = 5492.1246 DIHED =
> 13474.5652
> UB = 658.0292 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1442.6550 EEL = -33720.7957 HBOND =
> 0.0000
> 1-4 VDW = 2201.5174 1-4 EEL = 55772.1463 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4300 5.1745E+04 1.0075E+00 3.1358E+01 O4 646
>
> BOND = 6709.9190 ANGLE = 5443.8773 DIHED =
> 13470.0538
> UB = 656.5709 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1413.8174 EEL = -33917.3794 HBOND =
> 0.0000
> 1-4 VDW = 2195.8516 1-4 EEL = 55772.2527 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4350 5.1164E+04 1.2531E+00 7.0833E+01 O4 646
>
> BOND = 6704.4118 ANGLE = 5396.6303 DIHED =
> 13465.6141
> UB = 653.9261 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1384.2921 EEL = -34396.8933 HBOND =
> 0.0000
> 1-4 VDW = 2186.4101 1-4 EEL = 55769.7533 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4400 5.0996E+04 9.6524E-01 3.6889E+01 O4 646
>
> BOND = 6685.6632 ANGLE = 5353.4425 DIHED =
> 13454.9506
> UB = 651.3750 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1369.8349 EEL = -34476.3067 HBOND =
> 0.0000
> 1-4 VDW = 2180.5283 1-4 EEL = 55776.9901 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4450 5.0610E+04 1.0015E+00 4.2661E+01 O4 646
>
> BOND = 6671.8561 ANGLE = 5313.1393 DIHED =
> 13445.5516
> UB = 648.7829 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1352.5739 EEL = -34776.9856 HBOND =
> 0.0000
> 1-4 VDW = 2175.1915 1-4 EEL = 55779.5778 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4500 5.0365E+04 9.9913E-01 3.9785E+01 O4 646
>
> BOND = 6659.7642 ANGLE = 5270.4759 DIHED =
> 13433.8353
> UB = 646.4495 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1340.4119 EEL = -34936.5676 HBOND =
> 0.0000
> 1-4 VDW = 2170.0618 1-4 EEL = 55780.7906 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4550 5.0482E+04 1.0216E+00 3.7988E+01 O4 646
>
> BOND = 6649.5316 ANGLE = 5232.1966 DIHED =
> 13425.9793
> UB = 644.3352 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1327.3122 EEL = -34739.7507 HBOND =
> 0.0000
> 1-4 VDW = 2163.4585 1-4 EEL = 55779.3410 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4600 5.0252E+04 9.8965E-01 3.1319E+01 O4 646
>
> BOND = 6638.7812 ANGLE = 5198.0882 DIHED =
> 13418.9235
> UB = 642.0684 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1315.7633 EEL = -34900.2769 HBOND =
> 0.0000
> 1-4 VDW = 2156.8056 1-4 EEL = 55782.1110 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4650 5.0521E+04 9.8645E-01 2.9150E+01 O4 5266
>
> BOND = 6627.9695 ANGLE = 5165.1715 DIHED =
> 13413.6296
> UB = 640.1613 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1301.6467 EEL = -34564.4796 HBOND =
> 0.0000
> 1-4 VDW = 2151.7878 1-4 EEL = 55785.4055 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4700 5.0431E+04 8.9363E-01 2.6337E+01 O4 5266
>
> BOND = 6617.7364 ANGLE = 5136.0609 DIHED =
> 13410.4220
> UB = 638.1129 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1288.4499 EEL = -34588.0393 HBOND =
> 0.0000
> 1-4 VDW = 2145.4009 1-4 EEL = 55783.0160 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4750 5.0738E+04 8.9171E-01 2.6519E+01 O4 5266
>
> BOND = 6609.9103 ANGLE = 5111.7397 DIHED =
> 13407.1006
> UB = 636.3837 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1274.9029 EEL = -34224.8260 HBOND =
> 0.0000
> 1-4 VDW = 2141.0724 1-4 EEL = 55782.0239 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4800 5.0692E+04 8.8256E-01 2.5640E+01 O4 5266
>
> BOND = 6603.4277 ANGLE = 5088.4851 DIHED =
> 13405.6259
> UB = 634.1986 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1263.4759 EEL = -34216.8120 HBOND =
> 0.0000
> 1-4 VDW = 2135.0597 1-4 EEL = 55778.7790 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4850 5.0388E+04 8.6055E-01 2.5379E+01 O4 5266
>
> BOND = 6596.1235 ANGLE = 5067.2313 DIHED =
> 13402.4777
> UB = 632.0584 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1251.7949 EEL = -34470.2235 HBOND =
> 0.0000
> 1-4 VDW = 2130.1992 1-4 EEL = 55778.7279 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4900 4.9908E+04 8.7207E-01 2.6073E+01 O4 5266
>
> BOND = 6588.7898 ANGLE = 5044.8535 DIHED =
> 13397.5502
> UB = 630.5940 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1239.5219 EEL = -34900.9688 HBOND =
> 0.0000
> 1-4 VDW = 2126.9338 1-4 EEL = 55780.3764 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4950 5.0051E+04 8.4177E-01 2.5083E+01 O4 5266
>
> BOND = 6580.9815 ANGLE = 5025.0185 DIHED =
> 13396.1860
> UB = 629.0064 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1228.6435 EEL = -34709.0382 HBOND =
> 0.0000
> 1-4 VDW = 2123.0952 1-4 EEL = 55777.0798 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 5000 4.9376E+04 8.0457E-01 2.3946E+01 O4 5266
>
> BOND = 6573.5942 ANGLE = 5004.3572 DIHED =
> 13394.7651
> UB = 627.6383 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1217.2912 EEL = -35333.6879 HBOND =
> 0.0000
> 1-4 VDW = 2119.6786 1-4 EEL = 55772.4078 RESTRAINT =
> 0.0000
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 5000 4.9376E+04 8.0457E-01 2.3946E+01 O4 5266
>
> BOND = 6573.5942 ANGLE = 5004.3572 DIHED =
> 13394.7651
> UB = 627.6383 IMP = 0.0000 CMAP =
> 0.0000
> VDWAALS = 1217.2912 EEL = -35333.6879 HBOND =
> 0.0000
> 1-4 VDW = 2119.6786 1-4 EEL = 55772.4078 RESTRAINT =
> 0.0000
>
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
>
> --------------------------------------------------------------------------------
>
> | Build the list 11.42 (100.0% of List )
> | Other 0.00 ( 0.02% of List )
> | List time 11.42 ( 4.12% of Nonbo)
> | Short_ene time 262.56 (100.0% of Direc)
> | Other 0.19 ( 0.07% of Direc)
> | Direct Ewald time 262.75 (98.80% of Ewald)
> | Other 3.20 ( 1.20% of Ewald)
> | Ewald time 265.95 (95.88% of Nonbo)
> | Nonbond force 277.37 (89.31% of Force)
> | Bond/Angle/Dihedral 33.16 (10.68% of Force)
> | Other 0.03 ( 0.01% of Force)
> | Force time 310.56 (100.0% of Runmd)
> | Runmd Time 310.56 (99.06% of Total)
> | Other 2.93 ( 0.93% of Total)
> | Total time 313.50 (100.0% of ALL )
>
> | Number of list builds : 201
>
> | Highest rstack allocated: 3555
> | Highest istack allocated: 711
> | Job began at 05:36:19.100 on 12/12/2020
> | Setup done at 05:36:19.248 on 12/12/2020
> | Run done at 05:41:32.598 on 12/12/2020
> | wallclock() was called 115435 times
>
> |3D-RISM memory allocation summary
> |Type Maximum Current
> |Integer 0.00000 GB 0.00000 GB
> |Real 0.00000 GB 0.00000 GB
> |Logical 0.00000 GB 0.00000 GB
> |Character 0.00000 GB 0.00000 GB
> |---------------------------------------
> |Total 0.00000 GB 0.00000 GB
>
> On Fri, Dec 11, 2020 at 8:09 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Fri, Dec 11, 2020, Pinky Mazumder wrote:
> > >
> > >How can I convert (.psf) file into (.prmtop) and (incprd) to run
> > simulation
> > >in AMBER? I have made a cellulose bundle using a cellulose-builder. But
> > >this provides output as (.pdb) and (.psf) file? But, to perform
> simulation
> > >in AMBER, I need topology (.prmtop) and coordinates (.incprd) file.
> >
> > You have several options. I'm guessing you should try them in the
> > following order:
> >
> > 1. Use the chamber option in parmed (type 'help chamber' for info.)
> >
> > 2. See if the CHARMM-GUI likes the pdb file, and ask it to create
> > Amber inputs. Unlike option #1, this will get you the Amber force
> > field, not the CHARMM force field running in Amber.
> >
> > 3. Forget the .psf file, and build the system from the .pdb file using
> > tleap. This is likely to be the most difficult path, but you will
> > gain lots of useful experience about how Amber works, and will have
> > the most control over exactly what you get.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Pinky, Sharmi
> AL,US
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Dec 12 2020 - 13:00:02 PST
