AMBER Archive (2002)
Subject: (no subject)

From: deepak rangaswamy (deepak_ramu_at_yahoo.com)
Date: Tue Apr 02 2002 - 22:52:55 CST

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Previous message: darden: "Re: does PME function without charge neutralization?"
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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

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

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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Next message: Monica : "input files"
Previous message: darden: "Re: does PME function without charge neutralization?"
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AMBER Archive (2002)
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