[AMBER] Targeted MD - minimization problem

From: Jordan, Brad <jbjordan.amgen.com>
Date: Fri, 29 Oct 2010 09:33:51 -0700

Hi all - I'm attempting to fold a 160 residue protein from an extended strand structure towards a final structure (the target) using targeted MD. I have distance constraints that can be applied to do this. However, in my initial minimization step, I get LINMIN failure as below. Here are both my input file and the output file. Can anyone tell me what's going on? Any help is greatly appreciated.

Thanks,

Brad

Minimize.in

Stage 1 - minimisation of extended strand
 &cntrl
  imin=1, maxcyc=1000, ncyc=500,
  cut=999., igb=1, ntb=0,
  ntpr=100,
 &end




Output:


 Here is the input file:

Stage 1 - minimisation of TC5b
 &cntrl
  imin=1, maxcyc=1000, ncyc=500,
  cut=99999., igb=1, ntb=0,
  ntpr=100,
 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 10/28/10 Time = 09:28:41
 NATOM = 2634 NTYPES = 14 NBONH = 1337 MBONA = 1322
 NTHETH = 3040 MTHETA = 1792 NPHIH = 5646 MPHIA = 3355
 NHPARM = 0 NPARM = 0 NNB = 14598 NRES = 166
 NBONA = 1322 NTHETA = 1792 NPHIA = 3355 NUMBND = 42
 NUMANG = 89 NPTRA = 41 NATYP = 27 NPHB = 0
 IFBOX = 0 NMXRS = 25 IFCAP = 0 NEXTRA = 0


| Memory Use Allocated Used
| Real 20000000 97664
| Hollerith 400000 15972
| Integer 60000000 135769
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------



General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 1, ntb = 0, igb = 1, nsnb = 25
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut =**********, intdiel = 1.00000
     saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
     gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 1000, ncyc = 500, ntmin = 1
     dx0 = 0.01000, dxm = 0.50000, drms = 0.00010

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------


 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------



   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 NAN NAN 0.0000E+00 N 1

 BOND = 18948008.4414 ANGLE = 432.7759 DIHED = 1486.5571
 VDWAALS = ************* EEL = -26859.4121 EGB = nan
 1-4 VDW = 1985.1114 1-4 EEL = 6622.9339 RESTRAINT = 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
    100 NAN NAN 0.0000E+00 N 1

 BOND = nan ANGLE = nan DIHED = 747.7200
 VDWAALS = nan EEL = nan EGB = nan
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
    200 NAN NAN 0.0000E+00 N 1

 BOND = nan ANGLE = nan DIHED = 747.7200
 VDWAALS = nan EEL = nan EGB = nan
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
    300 NAN NAN 0.0000E+00 N 1

 BOND = nan ANGLE = nan DIHED = 747.7200
 VDWAALS = nan EEL = nan EGB = nan
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
    400 NAN NAN 0.0000E+00 N 1

 BOND = nan ANGLE = nan DIHED = 747.7200
 VDWAALS = nan EEL = nan EGB = nan
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000


   NSTEP ENERGY RMS GMAX NAME NUMBER
    500 NAN NAN 0.0000E+00 N 1

 BOND = nan ANGLE = nan DIHED = 747.7200
 VDWAALS = nan EEL = nan EGB = nan
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...


                    FINAL RESULTS



   NSTEP ENERGY RMS GMAX NAME NUMBER
    521 NAN NAN 0.0000E+00 N 1

 BOND = nan ANGLE = nan DIHED = 747.7200
 VDWAALS = nan EEL = nan EGB = nan
 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = 0.0000

     ***** REPEATED LINMIN FAILURE *****

--------------------------------------------------------------------------------
   5. TIMINGS
--------------------------------------------------------------------------------


| Highest rstack allocated: 28974
| Highest istack allocated: 5268

| Setup wallclock 1 seconds
| Nonsetup wallclock 283 seconds



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Received on Fri Oct 29 2010 - 10:00:02 PDT
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