Hello,
I am facing the problem with minimizing the protein
but it stops.
i am also attaching the output file of my sander
output.
Suggest me what is the solution.
Regards
Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan
tarisyed.yahoo.com
tarisyed.hotmail.com
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-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Tue Aug 7 17:33:35 2007
[-O]verwriting output
File Assignments:
| MDIN: min500res.in
| MDOUT: min500res.out
|INPCRD: a_wat.inpcrd
| PARM: a_wat.prmtop
|RESTRT: min500res.restrt
| REFC: a_wat.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Minimization Amber7
&cntrl
imin=1, maxcyc=500,
ntpr=5, ntr=1,
&end
Restraints
25.0
RES 1 602
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| New format PARM file being parsed.
| Version = 1.000 Date = 08/06/06 Time = 14:44:59
NATOM = 83966 NTYPES = 16 NBONH = 79131 MBONA = 4974
NTHETH = 10716 MTHETA = 6750 NPHIH = 20775 MPHIA = 15535
NHPARM = 0 NPARM = 0 NNB = 152047 NRES = 25407
NBONA = 4974 NTHETA = 6750 NPHIA = 15535 NUMBND = 44
NUMANG = 92 NPTRA = 48 NATYP = 31 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated Used
| Real 7000000 6930465
| Hollerith 1400000 529205
| Integer 7000000 6978695
| Max Nonbonded Pairs:64000000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
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 = 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
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 = 500, ncyc = 10, ntmin = 1
dx0 = 0.01000, dxm = 0.50000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
Box X = 104.886 Box Y = 109.197 Box Z = 87.672
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 120 NFFT3 = 90
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Restraints
GROUP 1 HAS HARMONIC CONSTRAINTS 25.00000
GRP 1 RES 1 TO 602
Number of atoms in this group = 9551
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 24805
Sum of charges from parm topology file = -0.00000058
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
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 = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 15030932
| TOTAL SIZE OF NONBOND LIST = 15030932
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.6263E+14 2.5407E+13 6.7020E+15 HA 5145
BOND = 10249.1760 ANGLE = 8398.2899 DIHED = 5699.4820
VDWAALS = ************* EEL = -282279.1775 HBOND = 0.0000
1-4 VDW = 394659.2423 1-4 EEL = 28526.4465 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 3.6659E+13 3.2816E+12 5.8665E+14 O 6336
BOND = 10249.2882 ANGLE = 8398.5289 DIHED = 5699.4731
VDWAALS = ************* EEL = -282301.0907 HBOND = 0.0000
1-4 VDW = 393870.5359 1-4 EEL = 28526.4664 RESTRAINT = 0.0173
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
10 2.7165E+12 1.4648E+11 2.3735E+13 CG2 8036
BOND = 10250.9075 ANGLE = 8399.2056 DIHED = 5699.5427
VDWAALS = ************* EEL = -282383.7977 HBOND = 0.0000
1-4 VDW = 392589.6778 1-4 EEL = 28526.3837 RESTRAINT = 0.2478
EAMBER = *************
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Received on Wed Aug 08 2007 - 06:07:37 PDT
