your initial energies are huge. how did you generate that input structure?
bond energies should not be that large, and vdw is "not a number".
On Fri, Oct 29, 2010 at 12:33 PM, Jordan, Brad <jbjordan.amgen.com> wrote:
> 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 - 10:00:03 PDT
