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
