[AMBER] Both positional and distance restraints

From: Damiano Spadoni <enxds6.nottingham.ac.uk>
Date: Wed, 13 Apr 2016 13:59:06 +0000

Dear all,

I am trying to run an MD simulation of my tetrameric protein while heating from 0 to 300K, applying positional restraints for some residues and distance restraints for other residues but the job stops.
Here I report the input file:

Stage 3 heating 0 to 300K with distance restraints on Fe4S4 - CYS
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10.0,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  ig = -1,
  gamma_ln = 1.0,
  nstlim = 500000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000
  nmropt = 1
 &end
 /
 &wt
   type = 'DUMPFREQ', istep1 = 50
 /
 DISANG = LAMPLP_RST.dist
 DUMPAVE = LAMPLP_dist.dat /
 &wt type = 'END'
 /
 Hold SAM and PLP
 50.0
 RES 1641 1642
 END
 Hold SAM and PLP
 50.0
 RES 1645 1646
 END
 Hold SAM and PLP
 50.0
 RES 1649 1650
 END
 Hold SAM and PLP
 50.0
 RES 1653 1654
 END
 END

While the output ends with:
   5. REFERENCE ATOM COORDINATES

  default_name
    ----- READING GROUP 1; TITLE:
  Hold

     GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
 GRP 1 RES 1641 TO 1642
      Number of atoms in this group = 94
    ----- READING GROUP 2; TITLE:
  Hold

     GROUP 2 HAS HARMONIC CONSTRAINTS 50.00000
 GRP 2 RES 1645 TO 1646
      Number of atoms in this group = 94
    ----- READING GROUP 3; TITLE:
  Hold

     GROUP 3 HAS HARMONIC CONSTRAINTS 50.00000
 GRP 3 RES 1649 TO 1650
      Number of atoms in this group = 94
    ----- READING GROUP 4; TITLE:
  Hold

     GROUP 4 HAS HARMONIC CONSTRAINTS 50.00000
 GRP 4 RES 1653 TO 1654
      Number of atoms in this group = 94
    ----- READING GROUP 5; TITLE:
  END

     GROUP 5 HAS HARMONIC CONSTRAINTS 0.00000

     rfree: End of file on unit 5

I found on the manual that should be the way apply pos. restraints to different groups of molecules, but it looks like can't read the distance restraints and is looking for other GROUP to read instead.
I am trying to run it using pmemd on a GPU with Amber14.
Is there anything am I doing wrong that I cannot see?

Any help would be appreciated.

Damiano







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Received on Wed Apr 13 2016 - 07:00:03 PDT
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