There is not a single solution because it is only a symptom on large forces.
Most likely you have parameter problems, or badly defined restraints. Set
ntpr to 1 and carefully examine the energies at each step.
On Mar 28, 2011 7:27 AM, "I.Haldoupis" <ih2g09.soton.ac.uk> 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
--
Best Regards,
Ioannis
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Received on Mon Mar 28 2011 - 06:00:04 PDT
