Dear All,
During the minimization of a small protein I am trying to use
the ibelly flag to keep all of the heavy atoms of the protein and some
of water molecules frozen, and the rest of solvent water molecules are
allowed to move. The input file is:
min
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 1000,
ntb = 1,
cut = 12,
ntpr=50,
ibelly=1,
bellymask='(:1-134.H) & (:135-4926)'
/
However, the minimization was stop only after 1000 steps, and an
error was occurred:
***** Processor 7
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 15781 Allocated: 3616
And the output file contains this:
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -2.2123E+05 NaN 0.0000E+00 N 1
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
VDWAALS = -122.1316 EEL = -221112.5317 HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
//Could you tell me where I have slipped up ?
Thank you very much for your help!
Best regards
Tong Zhu
--
Tong Zhu
------------------------------------------------------------------
State Key Laboratory of Precision Spectroscopy,
East China Normal University, Shanghai 200062, China and
Department of Physics, East China Normal University, Shanghai 200062, China
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Received on Fri Jul 08 2011 - 06:00:07 PDT
