AMBER Archive (2007)

Subject: Re: AMBER: Minimization amber9 segmentation fault

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Dec 01 2007 - 12:48:01 CST

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
>

      ____________________________________________________________________________________
Be a better pen pal.
Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu