In my protein some residues were missing, i added them and prepared
parameters of protein-ligand complex with explicit solvents using
ANTECHAMBER and tleap module of AMBER10, followed by dual minimization ; at
first minimizing the solvent molecule by applying the weight restraint to
protein, followed by minimization of whole system in second step. After
completion of min2 step, the last coordinates of restart files were 0.0000.
By same restart file i tired to euilibrate my system running the following
input file four times after 50ps of heating and 50 ps of density
equilibration with weak restraints on the complex followed by 500ps of
constant pressure equilibration at 300 .
'
&cntrl
imin=o, irest=1,ntx=5,
nstlim=1000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp=3000.0,
/
After completion of every job the coordinates of restart files were reducing
to 0.
System is not getting equilibrated even after 2ns run , RMSD is increasing
to 3angstorm, can i proceed with same to run production run.
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Received on Wed Sep 22 2010 - 02:00:03 PDT
