(no subject)

From: deepak rangaswamy <deepak_ramu_at_yahoo.com>
Date: Tue 2 Apr 2002 20:52:55 -0800 (PST)

Sir

i have some problem in running "md_ntr.in" for my
sysytem. i did initial minimization several times. i
have pasted the out put file below. please help me to
run "md_ntr.in" successfully.


thank you

sincerely
deepak

----------------------------------------------------


         
-------------------------------------------------------
          Amber 6 SANDER_CLASSIC
Scripps/UCSF 1999
         
-------------------------------------------------------

| Sat Nov 6 06:03:55 1999

  [-O]verwriting output

File Assignments:
|MDIN : md.ntr.in
                       
|MDOUT: H3_DNA_WAT_md.ntr.out
                       
|INPCR: 4H3_DNA_WAT.ntr.restart
                       
|PARM : H3_DNA_WAT.prmtop
                       
|RESTR: H3_DNA_WAT_md.ntr.restart
                       
|REFC : 4H3_DNA_WAT.ntr.restart
                       
|MDVEL: mdvel
                       
|MDEN : mden
                       
|MDCRD: mdcrd
                       
|MDINF: mdinfo
                       


 Here is the input file:

5DNB, initial dynamics w/ belly on DNA, model1, 9.0
cut
 &cntrl
                        
                                                      
                        
  timlim = 999999., nmropt = 1,
                        
  ntx = 1, irest = 0, ntrx = 1,
ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0,
ntwe = 0,
  ntwxm = 0, ntwvm = 0, ntwem = 0, ioutfm = 0,
                        
  ntwprt = 0,
                        
                                                      
                        
  ntf = 2, ntb = 2, idiel = 1,
dielc = 1.0,
  cut = 9.0, ntnb = 1, nsnb = 10,
ntid = 0,
  scnb = 2.0, scee = 1.2, cut2nd = 0.0,
ichdna = 0,
                                                      
                        
  isftrp = 0, rwell = 0.0,
                        
                                                      
                        
  ipol = 0,
                        
                                                      
                        
  ibelly = 0, ntr = 1,
                        
                                                      
                        
  imin = 0,
                        
  nrun = 1,
                        
  nstlim = 12500,
                        
  ndfmin = 0, ntcm = 0, nscm = 0,
                        
  init = 3, t = 0.0, dt = 0.002,
                        
                                                      
                        
  temp0 = 300.0, tempi = 100.0,
                        
  ig = 71277, heat = 0.0,
                        
  ntt = 1, isolvp = 0, dtemp = 0.0,
                        
  tautp = 0.2, tauts = 0.2,
                        
  vlimit = 20.0,
                        
                                                      
                        
  tauv0 = 0.0, tauv = 0.1, vzero = 0.0,
                        
                                                      
                        
  ntp = 1, pres0 = 1.0, comp = 44.6,
                        
  taup = 0.2, npscal = 1,
                        
                                                      
                        
  ntc = 2, tol = 0.00001,
                        
                                                      
                        
  imgslt = 0, iftres = 1,
                        
  jfastw = 0,
                        
                                                      
                        
  ivcap = 0, matcap = 0, fcap = 1.5,
                        
                                                      
                        
 &end
                        
 &wt
                        
   type='TEMP0', istep1=0, istep2=500,
                        
                 value1=100.0, value2=300.0,
                        
 &end
                        
 &wt
                        
   type='TEMP0', istep1=500, istep2=12500,
                        
                 value1=300.0, value2=300.0,
                        
 &end
                        
 &wt
                        
   type='END',
                        
 &end
                        
 &rst
                        
   iat=0,
                        
 &end
                        
Hold the H3 AND DNA
                        
500.0
                        
RES 1 68
                        
END
                        
Hold the ions
                        
50.0
                        
RES 69 97
                        
END
                        
END
                        
-------------------------------------------------------------------------------

5DNB, initial dynamics w/ belly on DNA, model1, 9.0
cut

| Reading &cntrl namelist w/ machine lib



   1. RESOURCE USE:

 NATOM = 17079 NTYPES = 20 NBONH = 16122
MBONA = 1004
 NTHETH = 1547 MTHETA = 1480 NPHIH = 2734
MPHIA = 2430
 NHPARM = 0 NPARM = 0 NNB = 29456
NRES = 5249
 NBONA = 1004 NTHETA = 1480 NPHIA = 2430
NUMBND = 52
 NUMANG = 113 NPTRA = 46 NATYP = 32
NPHB = 1
 IFBOX = 1 NMXRS = 33 IFCAP = 0


| Memory type Allocated
| Real 683280
| Hollerith 141883
| Integer 414696 (static)

| Max Nonbonded Pairs: 3781156 packed 2 to a
machine word

     BOX TYPE: RECTILINEAR


   2. CONTROL DATA FOR THE RUN

                                                      
                         

     TIMLIM= 999999. IREST = 0 IBELLY=
0
     KFORM = 1 ICHDNA= 0 IMIN =
0
     IPOL = 0 IEWALD= 0

     NTX = 1 NTXO = 1
     IG = 71277 TEMPI = 100.00 HEAT =
0.000

     NTB = 2 IFTRES= 1 BOXX =
57.635
     BOXY = 76.851 BOXZ = 52.650

     NRUN = 1 NTT = 1 TEMP0 =
300.000
     DTEMP = 0.000 TAUTP = 0.200 TAUTS =
0.200
     ISOLVP= 0 VLIMIT= 20.000

     NTP = 1 PRES0 = 1.000 COMP =
44.600
     TAUP = 0.200 NPSCAL= 1

     NTCM = 0 NSCM = 9999999

     NSTLIM=12500 INIT = 3 NTU =
1
     T = 0.000 DT = 0.00200

     NTC = 2 TOL = 0.00001 JFASTW =
0

     NTF = 2 NTID = 0 NTNB =
1
     NSNB = 10 IDIEL = 1 IMGSLT=
0
     IPRR = 0 IPRW = 0 ITRSLU=
1

     CUT = 9.000 SCNB = 2.000
     SCEE = 1.200 DIELC = 1.000
     CUT2ND= 0.00000

     NTPR = 100 NTWR = 50 NTWX =
500
     NTWV = 0 NTWE = 0 NTWXM =
  0
     NTWVM = 0 NTWEM = 0 IOUTFM=
  0
     NTWPRT= 0 NTWPR0= 0

     NTR = 1 NTRX = 1
     TAUR = 0.00000 NMROPT= 1 ISFTRP=
0
     RWELL = 0.00000 PENCUT= 0.10000

     IVCAP = 0 MATCAP= 0 FCAP =
1.500
     IRDARC= 0 IRD1ST= 0 IRDLST=
0
     IWRTSM= 0

   OTHER DATA:

     IFCAP = 0 NATCAP= 0 CUTCAP=
0.000
     XCAP = 0.000 YCAP = 0.000 ZCAP =
0.000

     NATOM = 17079 NRES = 5249

     Water definition for fast triangulated model:
     Resname = WAT ; Oxygen_name = O ; Hyd1_name =
H1 ; Hyd2_name = H2

     GFTIM = 2.00000 RLMAVF= 0.00000
ISGDEP= 3
     NMRAFA= 0 ILTAVF= 0

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5. REFERENCE ATOM COORDINATES

                                                      
                           
    ----- READING GROUP 1; TITLE:
 Hold the H3 AND DNA
                      

     GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
 GRP 1 RES 1 TO 68
      Number of atoms in this group = 1594
    ----- READING GROUP 2; TITLE:
 Hold the ions
                      

     GROUP 2 HAS HARMONIC CONSTRAINTS 50.00000
 GRP 2 RES 69 TO 97
      Number of atoms in this group = 29
    ----- END OF GROUP READ -----
Ligand Grid: OFF (not requested)

   3. ATOMIC COORDINATES AND VELOCITIES

                                                      
                         
 begin time read from input coords = 0.000 ps



           Begin reading energy term weight
changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 0 500 100.000000 300.000000 0
     0
 TEMP0 500 12500 300.000000 300.000000 0
     0

 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

                  Done reading weight changes/NMR
restraints


 Number of triangulated 3-point waters found: 5152
 Using 5152 waters for fast wat-wat

 Solute/solvent pointers:
     IPTSOL= 97 NATRCM= 1623
     IPTRES= 0 IPTATM= 0
     NSPSOL= 33 NSPSTR= 1623
     NSOLUT=17079 NATOM =17079


   KE Trans = 0.7443 KE Rot = 0.4657
C.O.M. Vel = 0.003727
 NB-update: NPAIRS = 2632887 HBPAIR = 818012

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
144.38 PRESS = -1809.93
 Etot = -72477.3206 EKtot = 5037.4569 EPtot
    = -77514.7775
 BOND = 124.5058 ANGLE = 928.8553 DIHED
    = 716.1801
 1-4 NB = 617.2227 1-4 EEL = -2135.4016
VDWAALS = 14602.4533
 EELEC = -92368.5932 EHBOND = 0.0000
CONSTRAINT = 0.0000
 EKCMT = 1501.2985 VIRIAL = 10614.6394 VOLUME
    = 233204.6585
                                               
Density = 0.7631

------------------------------------------------------------------------------

===============================================================================
                      NMR restraints for step 0
 Energy (this step): Bond = 0.000 Angle =
0.000 Torsion = 0.000
 Energy (tot. run) : Bond = 0.000 Angle =
0.000 Torsion = 0.000

 DEVIATIONS: Target=(r2+r3)/2
Target = closer of r2/r3
            This step Entire run This
step Entire run
           ave. rms ave. rms ave.
rms ave. rms
 Bond 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
 Angle 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
 Torsion 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
===============================================================================
 vlimit exceeded for step 1; vmax =
583.0307049375926

     COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
     DEVIATION IS TOO LARGE
     NITER, NIT, LL, I AND J ARE : 0 4 373 1014
1015

      A V E R A G E S O V E R 1 S T E P S


 NSTEP = 1 TIME(PS) = 0.002 TEMP(K) =
144.38 PRESS = -1809.85
 Etot = -72477.3206 EKtot = 5037.4569 EPtot
    = -77514.7775
 BOND = 124.5058 ANGLE = 928.8553 DIHED
    = 716.1801
 1-4 NB = 617.2227 1-4 EEL = -2135.4016
VDWAALS = 14602.4533
 EELEC = -92368.5932 EHBOND = 0.0000
CONSTRAINT = 0.0000
 EKCMT = 1501.7386 VIRIAL = 10614.6394 VOLUME
    = 233204.6585
                                               
Density = 0.7631

------------------------------------------------------------------------------

===============================================================================
                      NMR restraints for step 2
 Energy (this step): Bond = 0.000 Angle =
0.000 Torsion = 0.000
 Energy (tot. run) : Bond = 0.000 Angle =
0.000 Torsion = 0.000

 DEVIATIONS: Target=(r2+r3)/2
Target = closer of r2/r3
            This step Entire run This
step Entire run
           ave. rms ave. rms ave.
rms ave. rms
 Bond 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
 Angle 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
 Torsion 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
===============================================================================

      R M S F L U C T U A T I O N S


 NSTEP = 1 TIME(PS) = 0.002 TEMP(K) =
0.00 PRESS = 0.00
 Etot = 0.0000 EKtot = 0.0000 EPtot
    = 0.0000
 BOND = 0.0000 ANGLE = 0.0000 DIHED
    = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 0.0000
 EELEC = 0.0000 EHBOND = 0.0000
CONSTRAINT = 0.0000

------------------------------------------------------------------------------


 NMR restraints on final step:

 FATAL ERROR


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Received on Tue Apr 02 2002 - 20:52:55 PST
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