AMBER Archive (2008)

Subject: AMBER: amber9 hangas after job submission

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Aug 14 2008 - 01:40:03 CDT

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.

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| 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

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| 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

--------------------------------------------------------------------------------
   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 = 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 -----

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                               
 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...

--------------------------------------------------------------------------------
   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 = 0.3338E-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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