Re: [AMBER] Model building

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 22 Sep 2011 07:54:50 -0400

Hi,

Vlimit/SHAKE errors often indicate the system has not been adequately
minimized. What procedure did you use to minimize/equilibrate prior to
running MD? The SHAKE error message indicates that the problem is
between atoms 21 and 22 (the last two numbers in the NITER line). Have
you tried visualizing this part of the structure to see if everything
looks OK?

-Dan

On Thu, Sep 22, 2011 at 4:00 AM, Aparna P <aparnaspap.gmail.com> wrote:
> Hi
>
> I am working on Biomolecular modelling.i have build a model of a biomolecule
> and now i am doing MD of that.
> I have run the minimisation
> My input is
>
> DNA 10ps MD with res  10 kcal/mol restraints
>
>  &cntrl
>
>  imin   =
> 0,
>  irest  =
> 0,
>  ntx    =
> 1,
>  ntb    =
> 1,
>  cut    =
> 10,
>  ntr    =
> 1,
>  ntc    =
> 2,
>  ntf    =
> 2,
>  tempi  =
> 0.0,
>  temp0  =
> 150.0,
>  ntt    =
> 3,
>  gamma_ln =
> 1,
>  nstlim = 50000, dt =
> 0.001,
>  ntpr = 500, ntwx = 500, ntwr =
> 1000,
>  nmropt =
> 1,
>  /
>
>  &wt type = 'TEMP0', istep1  = 0, istep2 = 25000, value1 = 0.0, value2 =
> 150.0,
>  /
>
>  &wt type =
> 'END'
>  /
>
> Keep  DNA fixed with weak
> restraints
> 10.0
>
> RES 1
> 20
> END
>
> END
>
> But it shows Vlimit exeeding problem aftr some ps.as follows
>
> NSTEP =        0   TIME(PS) =       0.000  TEMP(K) =     0.00  PRESS =
> 0.0
>  Etot   =    -60915.8860  EKtot   =         0.0000  EPtot      =
> -60915.8860
>  BOND   =        46.0249  ANGLE   =       545.6061  DIHED      =
> 535.0389
>  1-4 NB =       259.1070  1-4 EEL =     -5583.3665  VDWAALS    =
> 10203.6931
>  EELEC  =    -66921.9894  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  Ewald error estimate:   0.2769E-03
>
> ------------------------------------------------------------------------------
>
>  NMR restraints: Bond =    0.000   Angle =     0.000   Torsion =     0.000
>
>
>  NSTEP =    10000   TIME(PS) =      20.000  TEMP(K) =    58.22  PRESS =
> 0.0
>  Etot   =    -51315.5240  EKtot   =      1479.8931  EPtot      =
> -52795.4171
>  BOND   =        75.7294  ANGLE   =       599.8928  DIHED      =
> 552.7123
>  1-4 NB =       272.6463  1-4 EEL =     -5596.9545  VDWAALS    =
> 8170.3153
>  EELEC  =    -56901.3723  EHBOND  =         0.0000  RESTRAINT  =
> 31.6135
>  EAMBER (non-restraint)  =    -52827.0306
>  Ewald error estimate:   0.8510E-04
>  -----------------------------------------------------------------------
>
> =======
> vlimit exceeded for step  10315; vmax =   256.3785
>
>     Coordinate resetting (SHAKE) cannot be accomplished,
>     deviation is too large
>     NITER, NIT, LL, I and J are :      0      0      4     21     22
>
>     Note: This is usually a symptom of some deeper
>     problem with the energetics of the system.
>
> I have used 1fs instad of 2 fs.then there was difference.But still it shows
> vlimit exeeding problem and now the programme got stopped itself.
> I have tried different input values.But I cannot tackle the problem.Is that
> because the structure is made by model building.?
> I have used the inprd structure as the reference structure.
>
> Kindly give me a suggestion.
>
> regrds
> Aparna.P
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>

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Received on Thu Sep 22 2011 - 05:00:03 PDT
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