[AMBER] Restraint removal doesn't seem to be happening

From: Daniel Burns <dburns.iastate.edu>
Date: Wed, 12 Jan 2022 16:42:04 -0500


I am trying to slowly release restraints that keep a small molecule properly coordinated with an iron atom in a protein active site.

When I run with an input file like I’ve pasted in the simulation continues to look restrained from istep1=50000001, istep2=100000000, value1=0.0, value2=0.0

  imin=0, irest=1, ntx=5, iwrap=1,
  nstlim=100000000, dt=0.002,
  ntc=2, ntf=2,
  cut=10.0, ntb=2, ntp=1, taup=1.0,
  ntpr=2000, ntwx=2000, ntwr= 2000,
  ntt=3, gamma_ln=2.0, temp0=303.15,
  ntr = 1, restraintmask =":479<:5&!.H=",
  restraint_wt = 1.0,
 &wt type='REST', istep1=0, istep2=50000000, value1=1.0, value2=0.0, &end
 &owt type='REST', istep1=50000001, istep2=100000000, value1=0.0, value2=0.0, &end
 &wt type='END' &end

When I restart from the end of this simulation with an input file that has no restraint terms, the protein immediately begins diffusing around and my iron pops out of proper coordination.

It seems like the above input doesn’t actually remove (or even change) the restraint terms.

Any ideas?

Thank you,


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Received on Wed Jan 12 2022 - 15:00:02 PST
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