AMBER Archive (2008)

Subject: Re: AMBER: equilibration

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Tue Oct 21 2008 - 06:17:08 CDT

yes the inpcrd is the same as the refc,
i changed the mask to restraintmask=':1-300_at_CA', restraint_wt=10
but the error is still the same:

Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 68 4641 4639

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

Urszula

> is the inpcrd the same as the refc?
> the mask looks odd- have you carefully checked the sander output to
> make sure it selects what you want?
>
>
> On Tue, Oct 21, 2008 at 6:44 AM, Urszula Uciechowska
> <urszula.uciechowska_at_pharmazie.uni-halle.de> wrote:
> > Dear amber users,
> >
> > I am trying to equilibrate the total volume of the water box for 20
> ps, at constant pressure (1atm) and
> > constant temperature (300K), and with positional restraints for CA
> and the crystal waters.
> > the input file:
> > &cntrl
> > imin = 0, irest = 0, ntx = 1,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 9, ntr = 1,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 25000, dt = 0.002,
> > ntpr = 50, ntwx = 50, ntwr = 50
> > restraintmask=':1-300_at_CA&:4799-40288', restraint_wt=10
> > /
> > I am getting such a error:
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 0 68 4641 4639
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
> > Could somebody help me to track the problem?
> >
> > Urszula
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> > to majordomo_at_scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu