[AMBER] MMPBSA.py nmode maxcyc problem

From: Niel Henriksen <niel.henriksen.utah.edu>
Date: Thu, 10 Jun 2010 08:51:08 -0600

I've been running gb, pb, and nmode analysis on an RNA/ligand system
using MMPBSA.py.MPI on two 8-core nodes (16 CPUs total).

my input file is:

  startframe=1, endframe=999999999, interval=1,
  receptor_mask=':1-38', ligand_mask=':39', strip_mdcrd=0,
  verbose=1, keep_files=1, entropy=1,
  igb=1, gbsa=1, saltcon=0.200,
  istrng=0.2, fillratio=4.0,
  nmode_igb=1, nmode_istrng=0.2, nminterval=200, maxcyc=1000,

The gb and pb calculations are fine. Most of the nmode calculations are okay.
But it looks like one of them won't finish. It reached the the maxcyc number of
iterations and then increased maxcyc by a factor of 10. All the rest of the
nmode tasks are finished except for this one and 10 hours later it is still running.
I have had several jobs do this and they keep running indefinitely.

First, why have a maxcyc if the program just increases it if it is reached?

Second, can you tell from the output what is going on with the calculation? It
looks like the CG minimization is dying. Is it probably just a bad structure that
won't minimize nicely? See out put at the bottom of this email.

Third, how do I know which pdb was used for the calculations that produced
_MMPBSA_complex_nm.out.5? (I guess I could search through the code, but
I'll try asking here first.) Is it the sixth pdb produced by ptraj? In my case
_MMPBSA_complex_nm.pdb.1001 ?

Fourth, any suggestions for how to prevent the problem or at least
terminate the program when the problem occurs?

Thanks for the help

OUTPUT FROM _MMPBSA_complex_nm.out.5:

Reading parm file (com.topo)

        mm_options: ntpr=10000
        mm_options: diel=C
        mm_options: kappa=0.147010203727
        mm_options: cut=1000
        mm_options: gb=1
        mm_options: dielc=4.0
        mm_options: temp0=298.15
scaling charges by 0.500
      iter Total bad vdW elect nonpolar genBorn frms
ff: 0 -805.90 1966.92 -388.57 718.31 0.00 -3102.56 1.99e+01
 MIN: It= 0 E= -805.90 ( 19.856)
  CG: It= 5 ( 0.413)q :-)
  LS: i= 1 lhs_f= -759.27688 rhs_f= -0.15304093
            lhs_g= 18.930947 rhs_g= 1377.3683
  LS: step= 1 it= 1
 MIN: It= 1 E= -1565.18 ( 5.645)
  CG: It= 3 ( 0.473)q :-)
  LS: i= 1 lhs_f= -99.283686 rhs_f= -0.019840063
            lhs_g= 0.17934537 rhs_g= 178.56056
  LS: step= 1 it= 1
 MIN: It= 9702 E= -254.26 ( 0.013)
  CG: It= 1 (999.999)q :-((
  LS: i= 1 lhs_f= 0.0010889731 rhs_f= -8.8553167e-08
            lhs_g= 0.0021649181 rhs_g= 0.0007969785
  LS: i= 2 lhs_f= 3.2271245e-05 rhs_f= -1.4808629e-08
            lhs_g= 0.00073717487 rhs_g= 0.0007969785
  LS: i= 3 lhs_f= 1.2717392e-06 rhs_f= -2.5536537e-09
            lhs_g= 0.00085998718 rhs_g= 0.0007969785
  LS: i= 4 lhs_f= 1.1181794e-07 rhs_f= -5.1091314e-10
            lhs_g= 0.00088042224 rhs_g= 0.0007969785
  LS: i= 5 lhs_f= 1.7803018e-08 rhs_f= -1.0507513e-10
            lhs_g= 0.00088448091 rhs_g= 0.0007969785
  LS: i= 6 lhs_f= 4.0517989e-09 rhs_f= -2.1713693e-11
            lhs_g= 0.00088531453 rhs_g= 0.0007969785
  LS: i= 7 lhs_f= 1.4933903e-09 rhs_f= -4.4752754e-12
            lhs_g= 0.00088548692 rhs_g= 0.0007969785
  LS: i= 8 lhs_f= 9.0960839e-10 rhs_f= -9.0468856e-13
            lhs_g= 0.00088552262 rhs_g= 0.0007969785
  LS: i= 9 lhs_f= 7.8819085e-10 rhs_f= -1.6832494e-13
            lhs_g= 0.00088552999 rhs_g= 0.0007969785
  LS: i=10 lhs_f= 7.7579898e-10 rhs_f= -2.1976357e-14
            lhs_g= 0.00088553145 rhs_g= 0.0007969785
  LS: i=11 lhs_f= 7.8921403e-10 rhs_f= -8.4068087e-16
            lhs_g= 0.00088553166 rhs_g= 0.0007969785
  LS: i=12 lhs_f= 7.6067863e-10 rhs_f= -1.4793792e-18
            lhs_g= 0.00088553167 rhs_g= 0.0007969785
  LS: i=13 lhs_f= 7.5692697e-10 rhs_f= -4.7951204e-24
            lhs_g= 0.00088553167 rhs_g= 0.0007969785
  LS: i=14 lhs_f= 7.5692697e-10 rhs_f= -8.8553167e-28
            lhs_g= 0.00088553167 rhs_g= 0.0007969785
  LS: step= 1e-20 it=14

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Received on Thu Jun 10 2010 - 08:00:05 PDT
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