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
>
>
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Received on Mon Mar 28 2011 - 06:00:05 PDT
