Hello Sir,
I have previously simulated similar system successfully. As per your
suggestion, i tried to do the same, but the error persists.
Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
On Sun, Oct 16, 2016 at 5:31 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> using modified residues can present new challenges. Have you already
> successfully used Amber to build an equilibrate a similar system using only
> standard residues? that can help you separate issues arising from your
> inputs and equilibration protocol from those in the modified parameter
> files.
>
> On Sun, Oct 16, 2016 at 5:10 AM, Prayagraj Fandilolu <fprayagraj.gmail.com
> >
> 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:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Oct 19 2016 - 03:30:03 PDT
