Dear Daniel:
The following is the input for the equilibriation procedure i followed.
initial minimisation solvent
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 1,
cut = 15
/
Hold the protein fixed
500.0
RES 1 42
END
END
initial minimisation whole system
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 0,
cut = 15
/
protein: heating
&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 = 2.0,
nstlim = 25000, dt = 0.002,
ntpr = 250, ntwx = 250, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 1 42
END
protein: density
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
cut = 10,
ntr = 1,
ntp = 1,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 25000, dt = 0.002,
ntpr = 250, ntwx = 250, ntwr = 1000
/
Keep protein fixed with weak restraints
5.0
RES 1 42
END
protein: equilibration
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
cut = 10,
ntp = 1,
ntc = 2,
ntf = 2,
taup = 2.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 250000, dt = 0.002,
ntpr = 500, ntwx = 500
/
I Changed ntx as 0 and irest as 1, and i tried once. but that too not
success same error
Harikrishna
On Wed, Jun 29, 2011 at 9:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This kind of error usually arises because your system has not been
> properly minimized. In particular, systems with explicit solvent
> require careful minimization and equilibration. If you post the
> minimization/equilibration procedure you have used to this point we
> may be able to make some recommendations.
>
> -Dan
>
> On Wed, Jun 29, 2011 at 11:06 AM, hari krishna <haricoolguy111.gmail.com>
> wrote:
> > Dear All:
> >
> > I am doing the MD simulation of the protein and RNA complex strucutre in
> the
> > presence of solvent. There is nothing wrong in the charge of the system,
> its
> > neutral only. But while heating the system its shows the following error
> > that shake cannot be accomplished and deeper problem in the energetics of
> > the system.
> >
> > I have used force field 99 and tried with force field 03 it shows the
> same
> > error. there is no modified force field applied to any of the system.
> >
> >
> > NITER, NIT, LL, I and J are : 0 0 636 9565 9564
> >
> >
> > What shall i do now
> >
> >
> > S.Harikrishna
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Wed Jun 29 2011 - 10:00:03 PDT
