AMBER Archive (2008)

Subject: Re: AMBER:

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Jul 04 2008 - 07:27:59 CDT

It is always the case in md.out the first results for NSTEPS=0 gives
RESTRAINT = 0.0000.
whether you specify restraints or not.

The pb is with the message amber gives me in the log:
     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 4583 9292 9293

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

> I'm still confused about the restrains- you define them in the
> md input but there is no restraint energy- why?
>
> On Fri, Jul 4, 2008 at 7:44 AM, Boutheina Kerkeni <b.kerkeni_at_ucl.ac.uk>
> wrote:
>>
>>
>>> 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 Å
>>
>>> 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_at_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_at_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
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------------------------------------------------
>>>>>> The AMBER Mail Reflector
>>>>>> To post, send mail to amber_at_scripps.edu
>>>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the
>>>>>> email)
>>>>>> to majordomo_at_scripps.edu
>>>>>>
>>>>> -----------------------------------------------------------------------
>>>>> The AMBER Mail Reflector
>>>>> To post, send mail to amber_at_scripps.edu
>>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>>>> to majordomo_at_scripps.edu
>>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------------
>>>> The AMBER Mail Reflector
>>>> To post, send mail to amber_at_scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>>> to majordomo_at_scripps.edu
>>>>
>>>
>>>
>>>
>>> --
>>> ===================================================================
>>> 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_at_gmail.com
>>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>>> ===================================================================
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>
>
>
> --
> ===================================================================
> 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_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu