AMBER Archive (2007)

Subject: Fwd: Re: AMBER: Minimization amber9 segmentation fault

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Dec 03 2007 - 10:30:11 CST

I removed all WAT residues at a distance <=1.5A from POPC residues from the
membrane already bearing a cavity. Then inserted the protein-complex and built
the TIP3P box with leap. Then run the minimization again. Starting energy was 9
orders of magnitude less that previous run (which had crashed because WAT 534
had clashes with POP 24) and gradient and energy decreased by only 2 orders of
magnitude. Again segmentation fault.

My first question about min.out below is whether NAME/NUMBER before step 16,
where segmentation fault occurred) were resolved by the minimization. C216/6440
relates to clashes at <=1.5A between various atoms of POPC 49 with WAT 2873. I
find curious clash between POPC 49 nitrogen and various WAT (N is shielded).

My second question is why now is the minimization is unable to complete the few
20 steps requested. If feeling is because of bad membrane, the procedure of
cleaning that I have followed is hopeless. I do not even know if present
clashes are with water inserted by leap.

Incidentally, Find Clashes at <=1.5 also detected interaction between C14 of
POPC 14 with TYR 355 OH.

Thanks
francesco

Below min.out:

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

| Run on 12/03/2007 at 12:31:09
  [-O]verwriting output

File Assignments:
| MDIN: box_min1.in
| MDOUT: box_min1.out
|INPCRD: protein_ligand_pop_box.inpcrd
   
| PARM: protein_ligand_pop_box.prmtop
   
|RESTRT: box_min1.rst
| REFC: protein_ligand_pop_box.inpcrd
   
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 
 Here is the input file:
 
1st minimization protein_ligand_pop_box80x80
   
 &cntrl
  imin=1, maxcyc=20, ncyc=10,
  cut=10, ntb=1, ntpr=1,
  ntr=1, restraintmask=":77-520, 521",
  restraint_wt=30,
  /
                                                                               
                                                                               

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

| Flags: MPI

 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 = 46.090
| New format PARM file being parsed.
| Version = 1.000 Date = 12/03/07 Time = 11:54:14
 NATOM = 89852 NTYPES = 18 NBONH = 82430 MBONA = 7441
 NTHETH = 22945 MTHETA = 9352 NPHIH = 38729 MPHIA = 20393
 NHPARM = 0 NPARM = 0 NNB = 192480 NRES = 24743
 NBONA = 7441 NTHETA = 9352 NPHIA = 20393 NUMBND = 62
 NUMANG = 130 NPTRA = 58 NATYP = 44 NPHB = 1
 IFBOX = 1 NMXRS = 134 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 6105013
| Hollerith 563857
| Integer 3172395
| Max Pairs 12938688
| nblistReal 1078224
| nblist Int 3318262
| Total 134217 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 = 1, 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 = 20, 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 = 112.533 Box Y = 109.793 Box Z = 92.179
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 120 NFFT2 = 120 NFFT3 = 96
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

      
     Mask :77-520, 521; matches 7002 atoms

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

                                                                               

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 24222
| Atom division among processors:
| 0 22463 44927 67391 89852

     Sum of charges from parm topology file = -0.00074086
     Forcing neutrality...
| Running AMBER/MPI version on 4 nodes

--------------------------------------------------------------------------------
   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 = 6439157
| TOTAL SIZE OF NONBOND LIST = 25795872

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 4.4840E+09 2.4571E+08 8.2511E+10 C216 9120

 BOND = 149932.4186 ANGLE = 46211.6820 DIHED = 9161.8416
 VDWAALS = ************* EEL = -246175.6118 HBOND = 0.0000
 1-4 VDW = 29126.1421 1-4 EEL = 23905.1720 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      2 3.9048E+09 2.0230E+08 6.7017E+10 C216 9120

 BOND = 149931.5554 ANGLE = 46211.5418 DIHED = 9161.8433
 VDWAALS = ************* EEL = -246175.5893 HBOND = 0.0000
 1-4 VDW = 29126.1265 1-4 EEL = 23905.1716 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      3 3.3404E+09 1.6205E+08 5.2613E+10 C216 9120

 BOND = 149930.5506 ANGLE = 46211.3764 DIHED = 9161.8454
 VDWAALS = ************* EEL = -246175.5688 HBOND = 0.0000
 1-4 VDW = 29126.1039 1-4 EEL = 23905.1713 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      4 2.8053E+09 1.2625E+08 3.9806E+10 C216 9120

 BOND = 149929.3939 ANGLE = 46211.1816 DIHED = 9161.8479
 VDWAALS = ************* EEL = -246175.5549 HBOND = 0.0000
 1-4 VDW = 29126.0704 1-4 EEL = 23905.1709 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      5 2.3119E+09 9.5708E+07 2.8972E+10 C216 9120

 BOND = 149928.0834 ANGLE = 46210.9519 DIHED = 9161.8508
 VDWAALS = ************* EEL = -246175.5562 HBOND = 0.0000
 1-4 VDW = 29126.0191 1-4 EEL = 23905.1707 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      6 1.8690E+09 7.0624E+07 2.0282E+10 C216 9120

 BOND = 149926.6314 ANGLE = 46210.6795 DIHED = 9161.8542
 VDWAALS = ************* EEL = -246175.5886 HBOND = 0.0000
 1-4 VDW = 29125.9383 1-4 EEL = 23905.1707 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      7 1.4821E+09 5.0684E+07 1.3673E+10 C216 9120

 BOND = 149925.0705 ANGLE = 46210.3512 DIHED = 9161.8581
 VDWAALS = ************* EEL = -246175.6813 HBOND = 0.0000
 1-4 VDW = 29125.8080 1-4 EEL = 23905.1713 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      8 1.1536E+09 3.5331E+07 8.8893E+09 C216 9120

 BOND = 149923.4609 ANGLE = 46209.9425 DIHED = 9161.8625
 VDWAALS = ************* EEL = -246175.8865 HBOND = 0.0000
 1-4 VDW = 29125.5930 1-4 EEL = 23905.1727 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      9 8.8260E+08 2.3952E+07 5.5816E+09 C216 9120

 BOND = 149921.9026 ANGLE = 46209.4065 DIHED = 9161.8671
 VDWAALS = ************* EEL = -246176.2982 HBOND = 0.0000
 1-4 VDW = 29125.2321 1-4 EEL = 23905.1760 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     10 6.6472E+08 1.5879E+07 3.3918E+09 C216 9120

 BOND = 149920.5592 ANGLE = 46208.6582 DIHED = 9161.8712
 VDWAALS = ************* EEL = -246177.0775 HBOND = 0.0000
 1-4 VDW = 29124.6222 1-4 EEL = 23905.1823 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     11 4.9271E+08 1.0388E+07 2.0041E+09 C216 9120

 BOND = 149919.6814 ANGLE = 46207.5601 DIHED = 9161.8722
 VDWAALS = ************* EEL = -246178.4803 HBOND = 0.0000
 1-4 VDW = 29123.6064 1-4 EEL = 23905.1941 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     12 4.9271E+08 1.0388E+07 2.0041E+09 C216 9120

 BOND = 149919.6814 ANGLE = 46207.5601 DIHED = 9161.8722
 VDWAALS = ************* EEL = -246178.4803 HBOND = 0.0000
 1-4 VDW = 29123.6064 1-4 EEL = 23905.1941 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     13 4.9270E+08 1.0388E+07 2.0041E+09 C216 9120

 BOND = 149919.6814 ANGLE = 46207.5600 DIHED = 9161.8722
 VDWAALS = ************* EEL = -246178.4805 HBOND = 0.0000
 1-4 VDW = 29123.6063 1-4 EEL = 23905.1941 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     14 2.5752E+08 4.4152E+06 6.2810E+08 C216 9120

 BOND = 149920.2383 ANGLE = 46204.2682 DIHED = 9161.8623
 VDWAALS = ************* EEL = -246183.5637 HBOND = 0.0000
 1-4 VDW = 29120.1388 1-4 EEL = 23905.2386 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     15 1.5253E+08 2.3773E+06 2.6132E+08 H15S 9125

 BOND = 149923.7015 ANGLE = 46201.8316 DIHED = 9161.8655
 VDWAALS = ************* EEL = -246188.6211 HBOND = 0.0000
 1-4 VDW = 29116.6876 1-4 EEL = 23905.2856 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     16 9.2781E+07 1.3708E+06 1.7956E+08 C216 6440

 BOND = 149932.1896 ANGLE = 46200.2690 DIHED = 9161.8888
 VDWAALS = 92768549.1604 EEL = -246194.5386 HBOND = 0.0000
 1-4 VDW = 29112.6552 1-4 EEL = 23905.3443 RESTRAINT = 0.0000
 EAMBER = 92780666.9688
---------------------------------------------------------END min.out.

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Sun, 2 Dec 2007 01:51:42 -0800 (PST)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Re: AMBER: Minimization amber9 segmentation fault
> To: amber_at_scripps.edu
>
> Adrian:
> I badly forgot to ask if a rule-of-thumb exists to establish a safe distance
> between the molecules to let minimization/MD go on (conditions related to the
> min.in that was included in the reported min.out).
>
> I checked that clashes exist between WAT and POPC residues in the membrane as
> built with the plugin (386 clashes for vdw >=0.6A for a 80x80A membrane; the
> number drops to 276 for vdw >=1.0A). That is, clashes occur in the
> intermediate
> region between the protein-complex and the external layer of WAT only. I
> can't
> imagine another alternative than removing those clashing WAT residues (the
> plugin does not offer options as fas as I could understand). Then, leap
> should
> refill WAT at right positions when making the box.
>
> Thanks
> francesco
>
>
>
> --- Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
>
> > Francesco,
> > Yes, in general you should make sure there are no clashes before you
> > make the
> > inpcrd (the prmtop is of course not affected by this as it has no
> > geometry information).
> >
> > So the question is how you created the system and why it had clashes to
> > start with.
> >
> > adrian
> >
> >
> > Francesco Pietra wrote:
> > > Adrian:
> > > Thanks a lot.
> > >
> > > I had a look at "O 17223" (534 WAT residue) through Chimera (as I worked
> > with
> > > DOCK, I am more familiar with Chimera). It is <1.0A from lipidic residue
> > POP24.
> > >
> > > The 80x80 membrane comes from a VMD plugin, where the polar heads of POPC
> > are
> > > TIP3P hydrated. I did not check if steric clashes were already there
> before
> > > creating the cavity and inserting the protein-complex.
> > >
> > > A preliminary application of the steric-clashes-search in Chimera
> revealed
> > many
> > > instances of them. However, I never used that tool before and it was a
> > cursory
> > > investigation.
> > >
> > > This mail is to ask if steric clashes should be avoided from the model
> > before
> > > building prmtop/inpcrd, or if there is a trick to eliminate them after.
> > > Completely unfamiliar with such problems. If steric clashes were only a
> few
> > > with WAT residues, I could imagine just to delete from the pdb file the
> WAT
> > > residues involved and build prmtop/inpcrd again.
> > >
> > > Cheers
> > > francesco
> > >
> > >
> > > --- Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
> > >
> > >> Francesco,
> > >> Seems like a straight vdw clash.
> > >> Strat by loading the system onto vmd and look around atom "O
> > >> 17223" and
> > >> see if it is too close to someone else.
> > >>
> > >> The gradient there is HUGE, so I suspect that. There might be other
> > >> clashes after you look at that one
> > >>
> > >>
> > >> NSTEP ENERGY RMS GMAX NAME NUMBER
> > >> 1 2.8852E+18 1.4602E+18 3.9863E+20 O
> 17223
> > >>
> > >> BOND = 149932.7945 ANGLE = 46211.6820 DIHED =
> > >> 9161.8416
> > >> VDWAALS = ************* EEL = -246440.0364 HBOND =
> > >> 0.0000
> > >> 1-4 VDW = 29126.1421 1-4 EEL = 23905.1720 RESTRAINT =
> > >> 0.0000
> > >>
> > >> Then, after ONLY 12 steps minimization , you get
> > >> NSTEP ENERGY RMS GMAX NAME NUMBER
> > >> > 12 2.8815E+11 3.6643E+10 1.0002E+13 O
> > 17223
> > >> >
> > >> > BOND = 149938.5018 ANGLE = 46211.8441 DIHED =
> > >> 9161.8506
> > >> > VDWAALS = ************* EEL = -246163.7303 HBOND =
> > >> 0.0000
> > >> > 1-4 VDW = 29126.0930 1-4 EEL = 23905.1432 RESTRAINT =
> > >> 0.0000
> > >> > EAMBER = *************
> > >>
> > >> So, your total energy decreased by 7 orders of magnitude and gradient by
>
> > >> eight orders.
> > >>
> > >> I suspect the segmentation fault is due to numerical errors of handling
> > >> these large numbers, but cannot say for sure.
> > >>
> > >>
> > >> Adrian
> > >>
> > >>
> > >>
> > >> Francesco Pietra wrote:
> > >>> Does this huge energy in trial minimization mean steric clashes or
> simply
> > a
> > >> bad
> > >>> min.in? I am posting as I can't understand better the segmentation
> fault.
> > >>>
> > >>> The system is a protein with non-covalently-bound large non-polymeric
> > >> ligand,
> > >>> immersed in a POPC hydrated membrane, the whole hydrated (all water is
> > >> TIP3P).
> > >>> >From ambmask:
> > >>> 1-76 POPC
> > >>> 77-520 protein
> > >>> 521 ligand
> > >>> 522-9999 WAT
> > >>> **** WAT
> > >>>
> > >>> (the latter corresponds to 0-4759 WAT from pdb obtained with ambpdb,
> > >> otherwise
> > >>> residue number and name are the same).
> > >>>
> > >>> If relevant, should the last line of min.in end with a comma, as I did?
> > >> There
> > >>> are different versions to this regard on the web.
> > >>>
> > >>> Thanks for help
> > >>> francesco pietra
> > >>>
> > >>> -------------------------------------------------------
> > >>> Amber 9 SANDER 2006
> > >>> -------------------------------------------------------
> > >>>
> > >>> | Run on 12/01/2007 at 16:29:59
> > >>> [-O]verwriting output
> > >>>
> > >>> File Assignments:
> > >>> | MDIN: box_min1.in
>
> >
> > >>
> > >>> | MDOUT: box_min1.out
>
> >
> > >>
> > >>> |INPCRD: protein_ligand_pop_box.inpcrd
>
> >
> > >>
> > >>>
> > >>> | PARM: protein_ligand_pop_box.prmtop
>
> >
> > >>
> > >>>
> > >>> |RESTRT: box_min1.rst
>
> >
> > >>
> > >>> | REFC: protein_gam_pop_box.inpcrd
>
> >
> > >>
> > >>> | MDVEL: mdvel
>
> >
> > >>
> > >>> | MDEN: mden
>
> >
> > >>
> > >>> | MDCRD: mdcrd
>
> >
> > >>
> > >>> |MDINFO: mdinfo
>
> >
> > >>
> > >>> |INPDIP: inpdip
>
> >
> > >>
> > >>> |RSTDIP: rstdip
>
> >
> > >>
> > >>>
> > >>> Here is the input file:
> > >>>
> > >>> 1st minimization protein_ligand_pop_box80x80
>
> >
> > >>
> > >>>
> > >>> &cntrl
>
> >
> > >>
> > >>> imin=1, maxcyc=20, ncyc=10,
>
> >
> > >>
> > >>> cut=10, ntb=1, ntpr=1,
>
> >
> > >>
> > >>> ntr=1, restraintmask=":77-520, 521",
>
> >
> > >>
> > >>> restraint_wt=30,
>
> >
> > >>
> > >>> /
>
> >
> > >>
> > >>>
>
> >
> > >>
> > >>>
>
> >
> > >>
> > >>>
> > >
> >
>
--------------------------------------------------------------------------------
> > >>> 1. RESOURCE USE:
> > >>>
> > >
> >
>
--------------------------------------------------------------------------------
> > >>> | Flags: MPI
>
> >
> > >>
> > >>> 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 = 46.090
> > >>> | New format PARM file being parsed.
> > >>> | Version = 1.000 Date = 11/28/07 Time = 12:12:33
> > >>> NATOM = 89900 NTYPES = 18 NBONH = 82478 MBONA = 7441
> > >>> NTHETH = 22945 MTHETA = 9352 NPHIH = 38729 MPHIA = 20393
> > >>> NHPARM = 0 NPARM = 0 NNB = 192544 NRES = 24759
> > >>> NBONA = 7441 NTHETA = 9352 NPHIA = 20393 NUMBND = 62
> > >>> NUMANG = 130 NPTRA = 58 NATYP = 44 NPHB = 1
> > >>> IFBOX = 1 NMXRS = 134 IFCAP = 0 NEXTRA = 0
> > >>> NCOPY = 0
> > >>>
> > >>>
> > >>> | Memory Use Allocated
> > >>> | Real 6108229
> > >>> | Hollerith 564161
> > >>> | Integer 3173435
> > >>> | Max Pairs 12945600
> > >>> | nblistReal 1078800
> > >>> | nblist Int 3319286
> > >>> | Total 134283 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 = 1, 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 = 20, 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 = 112.533 Box Y = 109.793 Box Z = 92.179
> > >>> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > >>> NFFT1 = 120 NFFT2 = 120 NFFT3 = 96
> > >>> Cutoff= 10.000 Tol =0.100E-04
> > >>> Ewald Coefficient = 0.27511
> > >>> Interpolation order = 4
> > >>>
> > >>> LOADING THE CONSTRAINED ATOMS AS GROUPS
> > >>>
> > >>>
> > >>> 5. REFERENCE ATOM COORDINATES
> > >>>
> > >>>
> > >>> Mask :77-520, 521; matches 7002 atoms
> > >>>
> > >>>
> > >
> >
>
--------------------------------------------------------------------------------
> > >>> 3. ATOMIC COORDINATES AND VELOCITIES
> > >>>
> > >
> >
>
--------------------------------------------------------------------------------
> > >>>
>
> >
> > >>
> > >>> begin time read from input coords = 0.000 ps
> > >>>
> > >>> Number of triangulated 3-point waters found: 24238
> > >>> | Atom division among processors:
> > >>> | 0 22475 44951 67427 89900
> > >>>
> > >>> Sum of charges from parm topology file = -0.00074086
> > >>> Forcing neutrality...
> > >>> | Running AMBER/MPI version on 4 nodes
> > >>>
> > >>>
> > >>>
> > >
> >
>
--------------------------------------------------------------------------------
> > >>> 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 = 6454031
> > >>> | TOTAL SIZE OF NONBOND LIST = 25821257
> > >>>
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 1 2.8852E+18 1.4602E+18 3.9863E+20 O
> 17223
> > >>>
> > >>> BOND = 149932.7945 ANGLE = 46211.6820 DIHED =
> > >> 9161.8416
> > >>> VDWAALS = ************* EEL = -246440.0364 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1421 1-4 EEL = 23905.1720 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 2 8.2905E+17 3.7817E+17 1.0324E+20 O
> 17223
> > >>>
> > >>> BOND = 149932.8374 ANGLE = 46211.6729 DIHED =
> > >> 9161.8416
> > >>> VDWAALS = ************* EEL = -246403.3807 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1396 1-4 EEL = 23905.1707 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 3 2.1637E+17 8.8247E+16 2.4091E+19 O
> 17223
> > >>>
> > >>> BOND = 149932.9075 ANGLE = 46211.6637 DIHED =
> > >> 9161.8416
> > >>> VDWAALS = ************* EEL = -246367.9129 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1367 1-4 EEL = 23905.1692 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 4 5.1492E+16 1.8633E+16 5.0866E+18 O
> 17223
> > >>>
> > >>> BOND = 149933.0186 ANGLE = 46211.6549 DIHED =
> > >> 9161.8417
> > >>> VDWAALS = ************* EEL = -246334.1279 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1334 1-4 EEL = 23905.1675 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 5 1.1230E+16 3.5795E+15 9.7717E+17 O
> 17223
> > >>>
> > >>> BOND = 149933.1907 ANGLE = 46211.6479 DIHED =
> > >> 9161.8419
> > >>> VDWAALS = ************* EEL = -246302.4146 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1294 1-4 EEL = 23905.1654 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 6 2.2583E+15 6.2972E+14 1.7191E+17 O
> 17223
> > >>>
> > >>> BOND = 149933.4532 ANGLE = 46211.6443 DIHED =
> > >> 9161.8422
> > >>> VDWAALS = ************* EEL = -246273.0505 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1249 1-4 EEL = 23905.1629 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 7 4.2146E+14 1.0218E+14 2.7895E+16 O
> 17223
> > >>>
> > >>> BOND = 149933.8485 ANGLE = 46211.6471 DIHED =
> > >> 9161.8428
> > >>> VDWAALS = ************* EEL = -246246.1983 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1198 1-4 EEL = 23905.1600 RESTRAINT =
> > >> 0.0000
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 8 7.3514E+13 1.5407E+13 4.2061E+15 O
> 17223
> > >>>
> > >>> BOND = 149934.4390 ANGLE = 46211.6606 DIHED =
> > >> 9161.8438
> > >>> VDWAALS = ************* EEL = -246221.9135 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1140 1-4 EEL = 23905.1567 RESTRAINT =
> > >> 0.0000
> > >>> EAMBER = *************
> > >>>
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 9 1.2074E+13 2.1752E+12 5.9383E+14 O
> 17223
> > >>>
> > >>> BOND = 149935.3146 ANGLE = 46211.6910 DIHED =
> > >> 9161.8452
> > >>> VDWAALS = ************* EEL = -246200.1611 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1076 1-4 EEL = 23905.1528 RESTRAINT =
> > >> 0.0000
> > >>> EAMBER = *************
> > >>>
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 10 1.8860E+12 2.8967E+11 7.9077E+13 O
> 17223
> > >>>
> > >>> BOND = 149936.6064 ANGLE = 46211.7479 DIHED =
> > >> 9161.8474
> > >>> VDWAALS = ************* EEL = -246180.8298 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.1006 1-4 EEL = 23905.1483 RESTRAINT =
> > >> 0.0000
> > >>> EAMBER = *************
> > >>>
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 11 2.8815E+11 3.6643E+10 1.0002E+13 O
> 17223
> > >>>
> > >>> BOND = 149938.5018 ANGLE = 46211.8441 DIHED =
> > >> 9161.8506
> > >>> VDWAALS = ************* EEL = -246163.7303 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.0930 1-4 EEL = 23905.1432 RESTRAINT =
> > >> 0.0000
> > >>> EAMBER = *************
> > >>>
> > >>>
> > >>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > >>> 12 2.8815E+11 3.6643E+10 1.0002E+13 O
> 17223
> > >>>
> > >>> BOND = 149938.5018 ANGLE = 46211.8441 DIHED =
> > >> 9161.8506
> > >>> VDWAALS = ************* EEL = -246163.7303 HBOND =
> > >> 0.0000
> > >>> 1-4 VDW = 29126.0930 1-4 EEL = 23905.1432 RESTRAINT =
> > >> 0.0000
> > >>> EAMBER = *************
> > >>>
> > >>>
> > >>>
> > >>>
> > >
> >
>
____________________________________________________________________________________
> > >>> Never miss a thing. Make Yahoo your home page.
> > >>> http://www.yahoo.com/r/hs
> > >>> -----------------------------------------------------------------------
> > >>> The AMBER Mail Reflector
> > >>> To post, send mail to amber_at_scripps.edu
> > >>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >>>
> > >> --
> > >> Dr. Adrian E. Roitberg
> > >> Associate Professor
> > >> Quantum Theory Project and Department of Chemistry
> > >>
> > >> University of Florida PHONE 352 392-6972
> > >> P.O. Box 118435 FAX 352 392-8722
> > >> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> > >>
> >
> ============================================================================
> > >>
> > >> To announce that there must be no criticism of the president,
> > >> or that we are to stand by the president right or wrong,
> > >> is not only unpatriotic and servile, but is morally treasonable
> > >> to the American public."
> > >> -- Theodore Roosevelt
> > >> -----------------------------------------------------------------------
> > >> The AMBER Mail Reflector
> > >> To post, send mail to amber_at_scripps.edu
> > >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >>
> > >
> > >
> > >
> > >
> >
>
____________________________________________________________________________________
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> > > The AMBER Mail Reflector
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> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project and Department of Chemistry
> >
> > University of Florida PHONE 352 392-6972
> > P.O. Box 118435 FAX 352 392-8722
> > Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> >
> ============================================================================
> >
> > To announce that there must be no criticism of the president,
> > or that we are to stand by the president right or wrong,
> > is not only unpatriotic and servile, but is morally treasonable
> > to the American public."
> > -- Theodore Roosevelt
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
>
>
>
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