Dear Amber users,
when I start the equilibration run after heating a protein molecule (about
200 aminoacid residues), I receive the error message:
ERROR: Problem reading coordinates or velocities from
EndoH1N1_gb_heat3slow.rst
I could not understand line 1633 :
1525.3274188-173.5683801
718.8293045-836.78710421003.7855053************
*s in the inpcrd file often indicate an overflow of the Fortran format used
to store coordinates in the inpcrd/restart files. This often happens when
coordinates are not wrapped into the center cell (when iwrap = 0) and some
particles diffuse too far away. Try restarting from your last good restart
file and setting iwrap=1 or using a NetCDF restart file format. See the
Amber manual for details
Here are the asterisks:
1525.7343256-173.6190120 719.0223153-837.01779391004.0492559************
679.4202985 9.14955061646.6762693 742.9513976************ 456.7156485
-651.6670212 134.31713181725.18516571385.5565069************-822.2471921
My input file for equilibration:
Stage 4 equilibration of EndoH1N1 300K
&cntrl
imin=0, irest=1, ntx=5,
nstlim=50000, dt=0.001,
ntc=2, ntf=2,
nscm /= 0,
ntt=1, tautp=1.0,
tempi=300.0, temp0=300.0,
ntpr=50, ntwx=50,
ntb=0, igb=1,
iwrap=1,
cut=999.0,rgbmax=999.
/
the input file for the last heating stage:
Stage 3 heating of EndoH1N1 200K to 300K
&cntrl
imin=0, irest=1, ntx=5,
nstlim=10000, dt=0.001,
ntc=2, ntf=2,
ntt=1, tautp=1.0,
tempi=200.0, temp0=300.0,
ntpr=50, ntwx=50,
ntb=0, igb=1,
iwrap=1,
cut=999.0,rgbmax=999.
/
what should I change then?..
Thank you in advance,
Nick
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Received on Mon Oct 31 2016 - 12:00:02 PDT
