can you try to be more specific? you tried to do the same as what? are you
saying that previously it worked, but now the same inputs do not work?
if the inputs work with unmodified parameters but fail with modified
parameters, then most likely there is a problem with the modified
parameters, or perhaps with the input structure that you generated. You
should look at those.
On Wed, Oct 19, 2016 at 6:08 AM, Prayagraj Fandilolu <fprayagraj.gmail.com>
wrote:
> 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
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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Received on Wed Oct 19 2016 - 05:00:03 PDT
