Dear amber users,
My system contains Protein+ligand+0.150mM of salt.
after equilibration, I have repartitioned the mass of hydrogens (parmed).
After completion of the simulation, I could not able to visualize the
trajectory in any of the visualizers like VMD, chimera.
I tried to convert the trajectory into PDB format, Even then the converted
PDB file is also unusable.
The parameters am using is as follows,
&cntrl
nstlim=5000000, dt=0.004, ntx=5, irest=1,
ntpr=1000, ntwr=20000, ntwx=500,
temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ntxo=2, ig=-1, cut=9.0,
barostat=2, mcbarint=100, ntave=0,
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
&end
/
what would be the possible solution for this.
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Received on Mon Dec 31 2018 - 02:30:03 PST
