AMBER Archive (2006)

Subject: Re: AMBER: working with large strained system

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jul 06 2006 - 08:41:39 CDT

it seems reasonable but with that much initial energy you will
need to do a lot of checking to make sure that nothing has gone
wrong structurally. For example, you can get chirality inversions,
cis/trans isomerizations, etc. These might not show up in the
energy.

Tanya Johannsen wrote:

>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
>
>
>
>__________________________________________________
>Do You Yahoo!?
>Tired of spam? Yahoo! Mail has the best spam protection around
>http://mail.yahoo.com
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu