[AMBER] Error while umbrella sampling with distance restraint

From: Meekyum Olivia Kim <olivijuly.gmail.com>
Date: Thu, 25 Jul 2013 11:45:56 -0700


I'm trying to do umbrella sampling in implicit solvent with distance restraint to calculate the PMF while pulling out the ligand from the protein. I'm doing minimization with the adjusted distance between the ligand and the receptor center of mass defined in the restraint file, without SHAKE, then followed by two equilibration with SHAKE turned on. The first equilibration fixes the protein with a small force constant. But the first equilibration didn't start and I got this error message regardless of the distance between the ligand and protein:

| ERROR: I could not understand line 190
 13.2773028 9.5137563 26.5189041************ 404.8478369************

*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
particles diffuse very far away from each other. Make sure you are removing
center-of-mass translation (nscm /= 0) or check if you have multiple, mobile
molecules that have diffused very far away from each other. This condition is
highly unusual for non-periodic simulations.

My equilibration input file looks like:

  ntr=1, ig=-1, nmropt=1,
  nstlim = 100000, nscm=10,
  cut=30, igb=5, saltcon=0.1,
  ntx=1, irest=0, ntb=0, ntpr=500,
  dt=0.002, nrespa=1,
  ntt=3, tempi=0.0, temp0=300., gamma_ln=2.0,
  ntc=2, ntf=2, tol=0.000001,
  ntwr = 5000, ntwx=5000, ioutfm=1,


And my restraint file is:

rst iat=-1,-1, r1=4.6, r2=7.6, r3=7.6, r4=10.6, rk2=200, rk3=200, ialtd=0,
igr1=440,442,444,447,449,453,457,458,1796,1798,1800,1802,1806,1809,1813,1814,3491,3493,3495,3497,3501,3504,3508,3509,5142,5144,5146,5148,5152,5156,5157, igr2=6000,6001,6002,6003,6018,6020

where igr1 is for the protein center of mass and igr2 is for the ligand center of mass.
Would anyone give me some solutions? Thank you very much!

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Received on Thu Jul 25 2013 - 12:00:02 PDT
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