AMBER Archive (2007)

Subject: Re: AMBER: Minimization amber9 segmentation fault

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Dec 02 2007 - 03:51:42 CST

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 = *************
> >>>
> >>>
> >>>
> >>>
> >
>
____________________________________________________________________________________
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> >>>
> >> --
> >> 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
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> >>
> >
> >
> >
> >
>
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>
> --
> 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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