Dear Amber users,
I would like to pertube system (7 residues) in vacuum to nothing, but I am
forcing several problems:
My first calculations were performed in Amber 10 with the option ifsc=2 and
following input:
&cntrl
imin=0,
nstlim=200000,
dt=0.001,
irest=1,
ntx=5,
ntpr=1000,
ntwx=1000,
ntwr=1000,
ioutfm=1,
ig=RANDOM,
ntf=1,
ntb=0,
cut=20,
ntr=1,
icfe=0,
clambda=LAMBDA,
ntc=2,
ifsc=2,
crgmask='CRGMASK',
scmask='SCMASK',
&end
Hold the system fixed by restraints
50
RES 1 7
END
END
In my run script I am changing the masks according to the system (here
SCMASK=:1-7), and LAMBDA according to the current window.
All the simulations end with the error report:
Frac coord min, max: 0.167951042129902 1.00004556442007
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
Can you help me please to fix this problem?
On the other hand, I would like to run all TI simulations in amber 11. Since
ifsc=2 option is no more implemented in this version, I would like to ask,
how to set up such simulation. I have tried to prepare empty restart file
and empty topology file representing process V1, but I did not work.
Thank you for you suggestions, Zora
--
==========================================
Zora Strelcova
==========================================
National Centre for Biomolecular Research (NCBR)
Faculty of Science, Masaryk University
Kotlarska 2, 611 37 Brno, Czech Republic
=========================================
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Received on Wed May 25 2011 - 07:00:02 PDT
