Re: AMBER:

From: Boutheina Kerkeni <b.kerkeni.ucl.ac.uk>
Date: Fri, 4 Jul 2008 12:44:20 +0100 (BST)

> the bond energy here is really high. have you looked at the structure
> to see why? look at atom 5941, which has the Gmax
The distance between the orginal 5914 and final 6914 atom is 1.5

> it's hard to diagnose because the restraints might be holding it
> in a high energy structure. It is also difficult because you are mixing
> belly and restraints, so hard to visually check things.
> have you tried using only restraints, or is there some reason that
> part of the structure must be absolutely constrained?
>
yes, its geometry needs to be fixed. I trained the constraint approach for
it but it resulted in unphysical distorsion of part2.
> actually now that I look closer I am confused- why is the
> restraint energy zero if you are using restraints? are you sure they were
> read properly? look in the sander output.
>
Yes, what I copied was part of minimisation, so no restraints at all,
first one being restraints on protein only.

The md pb may be comes from the ibelly group, is it usual to run
successful md with ibelly?
Thanks
B
> On Fri, Jul 4, 2008 at 7:02 AM, Boutheina Kerkeni <b.kerkeni.ucl.ac.uk>
> wrote:
>> Thanks you so much for the suggestions.
>> This is the last part of my minimization output from which my md started
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 2500 -8.1802E+03 2.8384E-01 4.8230E+01 NH1 5914
>>
>> BOND = 42002.5713 ANGLE = 2640.3485 DIHED =
>> 6628.7767
>> VDWAALS = 284231.0709 EEL = -380927.6059 HBOND =
>> 0.0000
>> 1-4 VDW = 2527.0010 1-4 EEL = 34717.6394 RESTRAINT =
>> 0.0000
>>
>>
>> Maximum number of minimization cycles reached.
>>
>>
>> FINAL RESULTS
>>
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 2500 -8.1802E+03 2.8384E-01 4.8230E+01 NH1 5914
>>
>> BOND = 42002.5713 ANGLE = 2640.3485 DIHED =
>> 6628.7767
>> VDWAALS = 284231.0709 EEL = -380927.6059 HBOND =
>> 0.0000
>> 1-4 VDW = 2527.0010 1-4 EEL = 34717.6394 RESTRAINT =
>> 0.0000
>> I checked with VMD the minimized pdb file and it lookes fine, part1
>> moved
>> a little but part 2 frozen. Is there another check to make sure every
>> thing went fine?
>> - Also As you suggested I started from tempi=300 tempf=300
>> but still got the same error message
>> vlimit exceeded for step 1; vmax = 210.0493
>>
>>> it might be because you are heating from 0K to 300K very quickly.
>>> you might try slower heating, or assign tempi of at least 200K, maybe
>>> even 300K (it depends on your system and how careful you need to
>>> be with equilibration, but it's something to at least try in order to
>>> identify
>>> the problem).
>>>
>>> the initial bond and vdw energies are really high - are you sure the
>>> minimization went as well as you think? is the initial energy here the
>>> same
>>> as the final energy from minimization? the vdw seems too high, even
>>> with
>>> explicit water (which usually has large vdw but even larger negative
>>> electrostatic)
>>> carlos
>>>
>>> On Fri, Jul 4, 2008 at 6:34 AM, Boutheina Kerkeni <b.kerkeni.ucl.ac.uk>
>>> wrote:
>>>> Hi AMber Users
>>>>
>>>> I am running an first stage md on my system composed of a
>>>> [protein(part1)
>>>> + (part2) ] solvated and neutralized.
>>>>
>>>> I want part2 to be frozen, so I did using belly. Minimizations went
>>>> fine.
>>>> When I start the md job:
>>>>
>>>> &cntrl
>>>> imin = 0,
>>>> irest = 0,
>>>> ntx = 1,
>>>> ntb = 1,
>>>> cut = 10,
>>>> ntr = 1,
>>>> ntc = 2, ntf = 2,
>>>> tempi = 0.0,
>>>> temp0 = 300.0,
>>>> ntt = 3,
>>>> gamma_ln = 1.0,
>>>> nstlim = 10000, dt = 0.002,
>>>> ntpr = 100, ntwx = 100, ntwr = 1000,
>>>> ibelly=1
>>>> /
>>>> Keep protein fixed with weak restraints
>>>> 10.0
>>>> RES 1 796
>>>> END
>>>> END
>>>> Keep part2 fixed with belly
>>>> ATOM 1 12180 20821 80124
>>>> END
>>>> END
>>>>
>>>>
>>>> The calculation stops with an error :
>>>> --------------------------------------------------------------------------------
>>>> 4. RESULTS
>>>> --------------------------------------------------------------------------------
>>>>
>>>> ---------------------------------------------------
>>>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>>>> using 5000.0 points per unit in tabled values
>>>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>>>> | CHECK switch(x): max rel err = 0.3338E-14 at 2.509300
>>>> | CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
>>>> ---------------------------------------------------
>>>> | Local SIZE OF NONBOND LIST = 1429347
>>>> | TOTAL SIZE OF NONBOND LIST = 24009616
>>>>
>>>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
>>>> =
>>>> 0.0
>>>> Etot = -30003.2906 EKtot = 0.0000 EPtot =
>>>> -30003.2906
>>>> BOND = 20179.4792 ANGLE = 2640.3486 DIHED =
>>>> 6628.7767
>>>> 1-4 NB = 2527.0010 1-4 EEL = 34717.6394 VDWAALS =
>>>> 284231.0709
>>>> EELEC = -380927.6064 EHBOND = 0.0000 RESTRAINT =
>>>> 0.0000
>>>> Ewald error estimate: 0.2038E-04
>>>> ------------------------------------------------------------------------------
>>>>
>>>> vlimit exceeded for step 1; vmax = 214.0560
>>>>
>>>>
>>>> Also in the log file the following message appears
>>>> -------------------------------------------
>>>> Job started at Fri Jul 4 11:25:26 BST 2008
>>>> -------------------------------------------
>>>>
>>>>
>>>> Coordinate resetting (SHAKE) cannot be accomplished,
>>>> deviation is too large
>>>> NITER, NIT, LL, I and J are : 0 0 4824 9785 9787
>>>>
>>>> Note: This is usually a symptom of some deeper
>>>> problem with the energetics of the system.
>>>>
>>>> --------------------------------------------
>>>> Job finished at Fri Jul 4 11:25:46 BST 2008
>>>>
>>>>
>>>> Any idea if someone has already seen such a pb?
>>>> Thanks very much for your help!
>>>> Regards
>>>> Boutheina
>>>>
>>>>
>>>>
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>>
>>
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>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling.gmail.com
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Received on Sun Jul 06 2008 - 06:07:44 PDT
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