AMBER Archive (2009)

Subject: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10

From: Keith Van Nostrand (kifvan_at_yahoo.com)
Date: Fri Jul 10 2009 - 10:27:12 CDT


Amber List,
 
  I am attempting to run QM/MM NEB with PM3-PDDG on an RNA system with Amber 10.
 
  Inpcrd files for the starting and ending configuration are each copied 15 times to give a total of 30 images.
 
  My addles.in file is as follows:
 
file rprm name=(reactant.prmtop) read
file rcrd name=(cat_reactant15X-product15X.inpcrd) pack=30 read
file wprm name=(AA-NEB-30image.prmtop) wovr
file wcrd name=(AA-NEB-30image.inpcrd) wovr
action
omas
pimd
spac numc=30 pick #prt 1 587 done
*EOD
 
 
  My .in file is as follows:
 
NVT MD w/ position restraints (5 kcal/molA) and PME (sander)
 &cntrl
  nmropt = 0,
  ntx    = 1,       irest  = 0,
  ntpr   = 50,      ntwx   = 50,
  ntf    = 2,       ntb    = 0,       dielc  = 1,
  igb    = 1,
  cut    = 15.0,    saltcon= 0 , rgbmax =15.0,
  imin   = 0,
  maxcyc = 5000,
  ncyc   = 1000,
  dx0    = 0.1,     dxm    = 0.5,     drms   = 0.0001,
  nstlim = 1000,
  nscm   = 1000,
  t      = 0,   dt     = 0.002,
  temp0  = 300.0,   tempi  = 300,
  ig     = 1000,
  ntt    = 3,
  gamma_ln  = 100,
  vlimit = 20.0,
  ntp    = 0,       pres0  = 1.0,
  ntc    = 2,
  ineb = 1,
  skmin = 10, skmax = 10, tmode = 1,
  ifqnt = 1
/
 &qmmm
  qmmask = '@143-156,437-450',
  qmcharge = 0,
  qmcut = 8.0, qmshake = 0,
 
  qm_theory = 'PM3-PDDG', verbosity = 0,
 
  printcharges = 0, peptide_corr = 0,
 
  writepdb = 1,
  dftb_disper = 0
/
 &end
 
 
  I attempt to run the calculation on a linux cluster with amber10 sander.MPI and get the following error at the end of the output file:
 
| Flags: MPI
  *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
      THAT WERE CREATED BY ADDLES, WITH NPARM=1
      USE A VERSION COMPILED WITH –DLES
 
 
  I suspect the problem may be with addles and the prmtop file.  The same procedure with addles has worked for amber9 NEB using an MM force field.  I attempted to submit this above calculation using only the MM force field as well with amber10 and get the same error in the .out file, so I don’t think this problem is related to the QMMM settings.
 
  Does anyone have suggestions on how I may get PM3-PDDG QMMM NEB to work?
 
Sincerely,
Keith  Van Nostrand

      
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