Dear Ross ,
I used gcc compler and my machine is Linux AMD opteron based 64 bit archi
tecture and I am using serial envioronment.
This is output file--->
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Amber 9 SANDER 2006
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| Run on 04/30/2008 at 11:25:34
[-O]verwriting output
Here is the input file:
rho:initial minimization with Cartesian restraints for the solute
&cntrl
imin=1, maxcyc=200,
ntpr=5,
ntr=1,
restraint_wt=50.0,
restraintmask=':1-1944',
/
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1. RESOURCE USE:
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| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 53.237
| New format PARM file being parsed.
| Version = 1.000 Date = 04/28/08 Time = 17:03:16
NATOM = 148533 NTYPES = 17 NBONH = 133395 MBONA = 15360
NTHETH = 35322 MTHETA = 20712 NPHIH = 66444 MPHIA = 48360
NHPARM = 0 NPARM = 0 NNB = 326426 NRES = 41249
NBONA = 15360 NTHETA = 20712 NPHIA = 48360 NUMBND = 37
NUMANG = 73 NPTRA = 43 NATYP = 29 NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 9593084
| Hollerith 932449
| Integer 5480366
| Max Pairs 49511000
| nblistReal 1782396
| nblist Int 6518026
| Total 332784 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: TRUNCATED OCTAHEDRON
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2. CONTROL DATA FOR THE RUN
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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 = 5, 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 = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 200, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 130.403 Box Y = 130.403 Box Z = 130.403
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 144 NFFT2 = 135 NFFT3 = 135
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
Mask :1-1944; matches 30630 atoms
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3. ATOMIC COORDINATES AND VELOCITIES
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begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 39299
Sum of charges from parm topology file = -0.00000252
Forcing neutrality...
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4. RESULTS
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---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 27054460
| TOTAL SIZE OF NONBOND LIST = 27054460
NSTEP ENERGY RMS GMAX NAME NUMBER
1 7.3878E+08 5.4632E+07 2.1205E+10 O 50311
BOND = 635.4719 ANGLE = 3767.4121 DIHED =
18625.3499
VDWAALS = ************* EEL = -509956.6162 HBOND =
0.0000
1-4 VDW = 8179.5683 1-4 EEL = 79691.9336 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 2.1616E+08 1.3622E+07 5.2885E+09 O 50311
BOND = 635.6940 ANGLE = 3767.4299 DIHED =
18625.3509
VDWAALS = ************* EEL = -509932.1931 HBOND =
0.0000
1-4 VDW = 8179.5682 1-4 EEL = 79691.9342 RESTRAINT =
0.0180
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
10 2.2420E+07 6.0929E+05 2.0568E+08 O 50311
BOND = 638.8230 ANGLE = 3767.6609 DIHED =
18625.3735
VDWAALS = 22818599.3161 EEL = -509882.9377 HBOND =
0.0000
1-4 VDW = 8179.5563 1-4 EEL = 79691.9499 RESTRAINT =
0.2667
EAMBER = 22419619.7420
Hope, now you can understand my problem
Thanks in advance
Anamika
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Received on Sun May 04 2008 - 06:07:02 PDT
