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.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.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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>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>
>
>
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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.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
-----------------------------------------------------------------------
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Received on Sun Dec 02 2007 - 06:07:52 PST
