Please paste your mdin file here. Perhaps starting temp is too high.
Thanks,
Bill
On 10/16/16 2:10 AM, Prayagraj Fandilolu wrote:
> Dear all,
>
> I am preparing a RNA system for MD simulation. The system consists of 2
> modified RNA residues which are defined by Aduri et al.
>
>
> The protocol consists of 1. prior minimization 2.Equilibration 3.
> Minimization 4. Production MD
>
> I am getting a problem after the 1st minimization step when i try to go for
> equilibration commands. The job get abnormally terminated. Also, i checked
> the output PDB of the rst file which shows distorted residues.
>
> The mdout file shows something like this:
>
>
>
>
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>
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>
>
>
> * NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> -6863.0 Etot = -85749.1605 EKtot = 0.0000 EPtot =
> -85749.1605 BOND = 41.7370 ANGLE = 283.5417 DIHED
> = 717.1987 1-4 NB = 316.9032 1-4 EEL = -2462.2275
> VDWAALS = 11458.8455 EELEC = -96105.1590 EHBOND =
> 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL =
> 34271.8077 VOLUME =
> 231284.2068 Density
> = 0.8729 Ewald error estimate:
> 0.1272E-03 ------------------------------------------------------------------------------Coordinate
> resetting (SHAKE) cannot be accomplished,deviation is too largeNITER, NIT,
> LL, I and J are : 0 2 38 117 118 Note: This is
> usually a symptom of some deeper problem with the energetics of the
> system.*
>
> When i had a look into the rst file of the previous minimization run, i
> found that it cannot be opened or read.
>
> I have tried using the system on both versions of AMBER (10 and 16). The
> same error persists.
>
> I am not getting a clue into how this can happen??
>
> Thanks in advance......
>
> Mr. Prayagraj Fandilolu
> Research Scholar,
> Structural Bioinformatics Unit
> Department of Biochemistry
> Shivaji University, Kolhapur - 416004
> (MS) India
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Received on Sun Oct 16 2016 - 03:30:02 PDT
