Dear AMBER experts, I have been trying to run AMBER9 sander, but it did not. It stops in the beginning itself.
Here I give you the output.
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Amber 9 SANDER 2006
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| Run on 08/13/2008 at 17:51:12
[-O]verwriting output
File Assignments:
| MDIN: min1-WATER-fix.in
| MDOUT: min1-WATER-fix-min1.out
|INPCRD: cello-lyoHIGH.crd
| PARM: cello-lyoHIGH.top
|RESTRT: cello-lyoHIGH-min-02.rst
| REFC: cello-lyoHIGH.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: cello-lyoHIGH-min-01.traj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
betaMaltose-lyo-low water system-FIX the WATER and MINIMIsE the LIPID
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 500,
ntb = 1,
ntr = 1,
cut = 10
/
Hold the WATER fixed
500.0
RES 257 2056
END
END
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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 = 26.422
| New format PARM file being parsed.
| Version = 1.000 Date = 08/12/08 Time = 11:28:22
NATOM = 35136 NTYPES = 9 NBONH = 26176 MBONA = 9216
NTHETH = 27648 MTHETA = 12032 NPHIH = 45312 MPHIA = 21248
NHPARM = 0 NPARM = 0 NNB = 138752 NRES = 5056
NBONA = 9216 NTHETA = 12032 NPHIA = 21248 NUMBND = 9
NUMANG = 14 NPTRA = 20 NATYP = 9 NPHB = 1
IFBOX = 1 NMXRS = 81 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2334734
| Hollerith 215874
| Integer 2211637
| Max Pairs 20238336
| nblistReal 421632
| nblist Int 1948793
| Total 117685 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
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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 = 50, 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 = 10.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 2500, ncyc = 500, 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 = 64.892 Box Y = 169.023 Box Z = 52.843
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 64 NFFT2 = 180 NFFT3 = 54
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Hold the WATER fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
GRP 1 RES 257 TO 5056
Number of atoms in this group = 14400
----- END OF GROUP READ -----
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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: 4800
Sum of charges from parm topology file = 0.00000000
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 = 0.3338E-14 at 2.509280
| CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 8858382
| TOTAL SIZE OF NONBOND LIST = 8858382
*****************************************************************************
It stops there itself.
I cant figure it out what is the wrong here.
Thanks
Regards
Vijay.M
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Received on Sun Aug 17 2008 - 06:07:19 PDT
