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
