AMBER Archive (2006)

Subject: AMBER: working with large strained system

From: Tanya Johannsen (tanyajohannsen_at_yahoo.com)
Date: Wed Jul 05 2006 - 21:29:58 CDT

Dear AMBER community:

I was hoping that someone could give me advice about
AMBER's capabilities for working with a very big, very
strained system. I have a system of about 23,000 heavy
atoms (and it will be a lot bigger after I add
explicit solvent). The system is not a simple crystal
structure; we have actually performed some refinement
procedures on it to test a hypothesized conformational
change, and the resulting structure is rough, with a
lot of atoms that are close together and things
twisted in strange ways. I am hoping that an AMBER
minimization can correct these problems with the
structure. I have run a test implicit solvent
minimization on it to see if AMBER can work with the
system, and since I am new to AMBER and chemistry in
general, and I am not sure how to interpret the
results. The initial energy seems high, but the energy
then decreases in a manner that seems reasonable,
which makes me wonder if AMBER is managing the system
okay. I have cut and pasted the energy information
from the .out file below. If anyone could take a look
and give me their opinion on whether AMBER can work
with my structure, I would be very grateful.

Thank you in advance.

Tanya

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
      1 1.8815E+11 7.9681E+09 5.0864E+11
    CE1 14332

 BOND = 55589.3592 ANGLE = 12184.7419
DIHED = 24774.6027
 VDWAALS = ************* EEL = -182470.8752 EGB
       = -33528.9928
 1-4 VDW = 2621189.7868 1-4 EEL = 113699.2076
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
     50 8.3833E+04 6.0544E+01 1.1389E+04
    HB3 3770

 BOND = 75744.9071 ANGLE = 25839.7402
DIHED = 26387.7500
 VDWAALS = 41999.7549 EEL = -180985.1851 EGB
       = -35541.1377
 1-4 VDW = 17095.5974 1-4 EEL = 113291.9949
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    100 -7.6106E+04 6.7496E+00 9.2599E+02
    CG 3771

 BOND = 3106.6981 ANGLE = 9954.1219
DIHED = 25599.3076
 VDWAALS = -16534.4570 EEL = -184943.6352 EGB
       = -35606.2726
 1-4 VDW = 10899.0169 1-4 EEL = 111419.0978
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    150 -8.4320E+04 1.2693E+00 1.4612E+02
    CZ 20433

 BOND = 1835.2873 ANGLE = 7676.0222
DIHED = 25448.0611
 VDWAALS = -19223.5408 EEL = -183817.5302 EGB
       = -37124.0771
 1-4 VDW = 9931.3107 1-4 EEL = 110954.2732
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    200 -8.7352E+04 7.4818E-01 5.9198E+01
    CZ 20433

 BOND = 1635.7310 ANGLE = 6964.6978
DIHED = 25387.4683
 VDWAALS = -20400.7798 EEL = -183912.3048 EGB
       = -37147.9082
 1-4 VDW = 9489.7950 1-4 EEL = 110631.1782
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    250 -8.9041E+04 1.4376E+00 2.5339E+02
    CZ 20433

 BOND = 1585.4073 ANGLE = 6589.9043
DIHED = 25333.5975
 VDWAALS = -21062.1356 EEL = -183477.5794 EGB
       = -37639.9528
 1-4 VDW = 9244.6705 1-4 EEL = 110385.5562
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    300 -9.0398E+04 2.0106E+00 3.2813E+02
    CZ 20433

 BOND = 1579.8403 ANGLE = 6330.0117
DIHED = 25263.8565
 VDWAALS = -21473.3804 EEL = -183598.8337 EGB
       = -37754.2687
 1-4 VDW = 9094.2061 1-4 EEL = 110160.1273
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    350 -9.1548E+04 1.3105E+00 2.1914E+02
    CZ 20433

 BOND = 1506.5535 ANGLE = 6163.2312
DIHED = 25173.4086
 VDWAALS = -21679.4755 EEL = -184226.4901 EGB
       = -37502.3111
 1-4 VDW = 8996.4213 1-4 EEL = 110020.9911
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    400 -9.2264E+04 6.7804E-01 1.1356E+02
    CZ 20433

 BOND = 1479.0719 ANGLE = 6046.3070
DIHED = 25102.9873
 VDWAALS = -21872.8605 EEL = -183766.3511 EGB
       = -38142.6346
 1-4 VDW = 8911.5434 1-4 EEL = 109978.1407
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    450 -9.2786E+04 1.0530E+00 1.8439E+02
    CZ 20433

 BOND = 1477.7497 ANGLE = 5959.9209
DIHED = 25042.8409
 VDWAALS = -22037.0124 EEL = -182406.5580 EGB
       = -39603.2214
 1-4 VDW = 8846.2348 1-4 EEL = 109933.6735
RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    500 -9.3256E+04 3.2073E-01 1.8957E+01
    CZ 20433

 BOND = 1453.1128 ANGLE = 5884.2725
DIHED = 24989.7304
 VDWAALS = -22165.3787 EEL = -181834.5719 EGB
       = -40269.7803
 1-4 VDW = 8794.8717 1-4 EEL = 109892.0801
RESTRAINT = 0.0000

  Maximum number of minimization cycles reached.

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    500 -9.3256E+04 3.2073E-01 1.8957E+01
    CZ 20433

 BOND = 1453.1128 ANGLE = 5884.2725
DIHED = 24989.7304
 VDWAALS = -22165.3787 EEL = -181834.5719 EGB
       = -40269.7803
 1-4 VDW = 8794.8717 1-4 EEL = 109892.0801
RESTRAINT = 0.0000

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