Thank you all for your helpful comments and apologies for replying late.
I found, however, an issue with my protein structure that seems to be
causing the problem.
Thanks again for your input.
On Mon, 2011-03-28 at 16:32 +0100, Jason Swails wrote:
> I'll chime in with my comments here as well.
>
> Have you seen this? http://ambermd.org/Questions/linmin.html
>
> The issue with a linmin failure is that the minimizer couldn't find the
> appropriate direction to move the system in order to reduce the total
> energy. The xmin minimizer is much better than the builtin one. To use
> this, set ntmin=3. See the manual for more details.
>
> Note that if you're just trying to relax your structure in order to start
> dynamics, you structure *should* be good enough by the time you hit a linmin
> failure to just start running. I would only advocate using xmin if what you
> *really* needed was a minimization as close as possible to a local minimum.
>
> Hope this helps,
> Jason
>
> On Mon, Mar 28, 2011 at 5:40 AM, Hugh Heldenbrand <helde010.umn.edu> wrote:
>
> > Hello-
> >
> > The solution is to restart your minimization not from the beginning, but
> > from a restart file that is written for a point in your minimization
> > that occurs before the linmin failure.
> >
> > So, if your failure is occuring at step 653, set maxcyc=500 to get 500
> > steps of minimization and a restart file at the end. Then restart your
> > minimization using the restart file (not the original coordinate file)
> > with maxcyc=4500 to get the rest of the total 5000 steps. If another
> > linmin failure occurs, repeat.
> >
> > -Hugh Heldenbrand
> > Graduate Student
> > University of Minnesota
> >
> > On 03/28/2011 07:27 AM, I.Haldoupis wrote:
> > > Dear Amber users,
> > >
> > > As a part of reproducing some published work I need to minimize, using
> > > implicit solvation, a ligand in a protein keeping the protein
> > > constrained. Unfortunately I get the LINMIN error
> > >
> > > ".... RESTARTED DUE TO LINMIN FAILURE ...
> > >
> > > ***** REPEATED LINMIN FAILURE ***** "
> > >
> > > Looking through the mailing list I see it is a re-occurring issue and
> > > that there isn't a clear solution. I tried changing things such as
> > > increasing ncyc to 1000, or excluding the gbsa term, or expressing the
> > > restrain using the 'restraint_wt' and 'restraintmask' options, however I
> > > still get the same error eventually.
> > > I tried running it using xmin minimization (ntmin option 3) using the
> > > defaults, but terminated early - not sure if that is related to the
> > > default convergence criterion for the energy gradient (drms option under
> > > xmin).
> > >
> > > I am just learning Amber and any help would be much appreciated.
> > >
> > > Please find below my original minimization input file.
> > >
> > > Minimization with constrained protein
> > > &cntrl
> > > imin=1, maxcyc=5000, ncyc=100,
> > > ntpr=1,
> > > cut=16,
> > > ntb=0,ntr=1,
> > > igb=1,
> > > gbsa=1
> > > /
> > > Hold protein fixed
> > > 1000.0
> > > RES 1 254
> > > END
> > > END
> > >
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
--
Best Regards,
Ioannis Haldoupis
_____________________________
PhD Student
Jonathan W. Essex Group
School Of Chemistry
University of Southampton, SO17 1BJ
B27:2011
Email: ih2g09.soton.ac.uk
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Received on Tue Mar 29 2011 - 03:30:02 PDT
