Hi Carlos,
Thank you for your feedback.
Do you have any idea how I could fix this issue?
Thank you again!
Sincerely,
On Sat, Dec 12, 2020 at 2:53 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> >
> _______________________________________________
> 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
Received on Sat Dec 12 2020 - 13:00:03 PST
