AMBER Archive (2004)

Subject: AMBER: MD problem.

From: Osman Gani (osman.gani_at_fagmed.uit.no)
Date: Wed Mar 17 2004 - 05:07:47 CST

Dear Amber users,

I have been using AMBER 7 on HP SuperDome. I am trying to run MD of a LIGAND+PROTEIN complex. With other ligands, everything went well with the same PROTEIN. I guess, I am having problem in parameterization of my current LIGAND. I used PARMCHK in ANTECHAMBER (always using "-at amber") to get the parameters.In the " ATTN, need revision" space , I manually added some parameters in accordance with PARM99.dat.Initial minimization was ok. But MD stopped with error message-
     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 6 4 4055 4054

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

How can proceed now?

Thanks in advance for your suggestions.

Osman

Following is my MD output;

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Tue Mar 16 16:02:35 2004

  [-O]verwriting output

File Assignments:
| MDIN: md1.in
| MDOUT: p5wation.out3
|INPCRD: p5wation.rst2
| PARM: p5wation.top
|RESTRT: p5wation.rst3
| REFC: p5wation.rst2
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd3
|MDINFO: p5wation.inf
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

 1st dynamics on pdock1, 9.0 cut
 &cntrl

  nmropt = 1,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr =2000, ntwx =2000, ntwv = 0, ntwe = 0,
 ntwprt = 4055,
  ntf = 2, ntb = 1,
  cut = 9.0, nsnb = 10,

  ibelly = 0, ntr = 1,

  imin = 0,
 nstlim = 12500,

  t = 0.0, dt = 0.001,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,

 ntp= 0, pres0= 1.0, COMP = 44.6,
  taup = 0.2, npscal = 1,

  ntc = 2, tol = 0.00001,

 &end
 &wt
   type='TEMP0', istep1=0, istep2=1500,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=1500, istep2=12500,
                 value1=300.0, value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
Hold the pdock1 fixed
1
RES 1 256
END
END

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

| Flags: MEM_ALLOC MPI RLE ROWAT
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| New format PARM file being parsed.
| Version = 1.000 Date = 03/16/04 Time = 14:14:35
 NATOM = 34742 NTYPES = 17 NBONH = 32730 MBONA = 2055
 NTHETH = 4637 MTHETA = 2807 NPHIH = 8651 MPHIA = 5284
 NHPARM = 0 NPARM = 0 NNB = 63380 NRES = 10485
 NBONA = 2055 NTHETA = 2807 NPHIA = 5284 NUMBND = 65
 NUMANG = 139 NPTRA = 61 NATYP = 38 NPHB = 1
 IFBOX = 1 NMXRS = 70 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated
| Real 2565259
| Hollerith 218939
| Integer 2079862
| Max Pairs 3302971
| Max Rstack 2000000
| Max Istack 2000000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 0, nmropt = 1

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
     ntxo = 1, ntpr = 2000, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 2000, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 4055, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 1, igb = 0, nsnb = 10
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Molecular dynamics:
     nstlim = 12500, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 15.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 300.00000, tempi = 100.00000, heat = 0.00000
     dtemp = 5.00000, tautp = 0.20000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

NMR refinement options:
     iscale = 0, noeskp = 1, ipnlty = 1, mxcub = 1
     scalm = 100.00000, pencut = 0.10000, tausw = 0.10000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
   Box X = 84.291 Box Y = 73.396 Box Z = 70.636
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 90 NFFT2 = 75 NFFT3 = 72
     Cutoff= 9.000 Tol =0.100E-04
     Ewald Coefficient = 0.30768
     Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
 Hold the pdock1 fixed

     GROUP 1 HAS HARMONIC CONSTRAINTS 1.00000
 GRP 1 RES 1 TO 256
      Number of atoms in this group = 4055
    ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
   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 1500 100.000000 300.000000 0 0
 TEMP0 1500 12500 300.000000 300.000000 0 0
 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

| Reorder water Setup:
| ----- Reordering water will NOT be done
| NMROPT not equal 0
|
 Number of triangulated 3-point waters found: 10229
| Atom division among processors:
| 0 8687 17372 26057 34742
| Running AMBER/MPI version on 4 nodes

     Sum of charges from parm topology file = -0.00000008
     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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 2205126
| TOTAL SIZE OF NONBOND LIST = 7932399

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 146.00 PRESS = 0.0
 Etot = -124272.7466 EKtot = 10371.2229 EPtot = -134643.9695
 BOND = 113.6792 ANGLE = 514.1255 DIHED = 2273.8981
 1-4 NB = 862.4934 1-4 EEL = 10928.9458 VDWAALS = 17582.8130
 EELEC = -166919.9245 EHBOND = 0.0000 RESTRAINT = 0.0000
 Ewald error estimate: 0.8727E-04
 ------------------------------------------------------------------------------

===============================================================================
                      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
===============================================================================

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 6 4 4055 4054

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
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