Thanks
I tried to equilibrate what ever the box I have now. ( May be I can try the
truncated octahedral later.) But it won't allow me to do that and request
velocity info.
ERROR: I could not find enough velocities in
ethbox.inpcrd
Does that mean I must at least minimize few steps?
Chinthaka
On Tue, Jul 23, 2013 at 3:26 PM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> On Jul 23, 2013, at 3:10 PM, Chinthaka Ratnaweera wrote:
>
> > Ok
> > I used 'setbox ETHBOX vdw {5,5,5}'
> > It make a box bigger than previous.
> >
> > The box dimensions now read as
> >> setbox ETHBOX vdw {5,5,5}
> > Box dimensions: 65.435279 64.286901 64.791138
> >
> > my Packmol box should be 50*50*50. Is this size enough now?
> >
> > but this gives the same problem in minimization. Are you mean I have to
> do
> > the equilibration at constant pressure without minimization? I try that
> >
>
> I've been away from this stuff for a couple of years, so all I can comment
> is
> that the boxes set with LEaP and Packmol were not oriented the same (if I
> remember correctly.) I figured this out a couple of years ago, but the
> details
> are hazy. IIRC, the most foolproof way I found was to create (counter
> intuitively) an origin-centered sphere with the correct number of
> molecules.
>
> Then enclose the sphere with with a truncated octahedron substantially
> bigger
> than the sphere. If your packmol structure is not tightly packed, you can
> probably get away with no (or minimal) minimization. Of course the larger
> the truncated octahedron "box," the longer the constant pressure run to
> equilibrate the density.
>
> I MAY have had to make sure the trunc. oct. and the sphere were
> co-centered,
> I can't remember.
>
> After you get an equilibrated restart file, you can cut out an
> appropriately
> sized cube with ptraj (IIRC, although can't remember the exact commands.)
>
> Good luck,
> Bud Dodson
>
> PS, another way to do this is to use a PDB with only a single molecule,
> then
> "solvate" that molecule with more of the same molecule. This is probably
> less trouble than using Packmol for single species boxes. Packmol is
> needed
> for mixtures, though, I believe.
>
> > On Tue, Jul 23, 2013 at 2:52 PM, M. L. Dodson <mldodson.comcast.net>
> wrote:
> >
> >>
> >> On Jul 23, 2013, at 2:45 PM, M. L. Dodson wrote:
> >>
> >>>
> >>> On Jul 23, 2013, at 2:19 PM, Chinthaka Ratnaweera wrote:
> >>>
> >>>> I followed the procedure in tutorial 15.
> >>>>
> >>>> This is my packmol input file
> >>>>
> >>>> tolerance 2.0
> >>>> output ethbox.pdb
> >>>> filetype pdb
> >>>> structure ethanol.pdb
> >>>> number 1000 # Number of molecules
> >>>> inside cube 0. 0. 0. 50. # x, y, z coordinates of box, and length of
> >> box in
> >>>> Angstroms
> >>>> end structure
> >>>>
> >>>> Then use leap to generate initial coordinates and topologies.
> >>>> source leaprc.gaff
> >>>> ETH = loadmol2 ethanol.mol2
> >>>> ETHBOX = loadpdb ethbox.pdb
> >>>> setbox ETHBOX centers
> >>>> saveAmberParm ETHBOX ethbox.prmtop ethbox.inpcrd
> >>>>
> >>>> But when running minimization under NVT it gave me this error
> >>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >>>>
> >>>> my minimization input is
> >>>> test run 1
> >>>> &cntrl
> >>>> imin = 1, ntpr = 100, ntwx=100, maxcyc = 10000, ntb=1
> >>>> &end
> >>>>
> >>>> This starts the first step of minimization
> >>>> 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 = 1264139
> >>>> | TOTAL SIZE OF NONBOND LIST = 1264139
> >>>>
> >>>>
> >>>> NSTEP ENERGY RMS GMAX NAME NUMBER
> >>>> 1 2.1423E+09 4.7538E+08 4.7855E+10 H4 2698
> >>>>
> >>>> BOND = 547891.8779 ANGLE = 201752.1037 DIHED =
> >>>> 2455.8141
> >>>> VDWAALS = ************* EEL = 12317.8836 HBOND =
> >>>> 0.0000
> >>>> 1-4 VDW = 72044523.0714 1-4 EEL = -22796.8084 RESTRAINT =
> >>>> 0.0000
> >>>>
> >>>>
> >>>> Is this because of my box size?
> >>>>
> >>>>
> >>>
> >>> Probably not. Boxes created with packmol are not equilibrated with
> >> periodic boundaries.
> >>> Packmol just puts packs spheres (connected spheres in the case of
> >> ethanol.) At the
> >>> box boundaries, parts of molecules extend beyond the box. When the
> boxes
> >> are tiled,
> >>> some of the atoms overlap with the next image so you get VDW clashes.
> >> You need a box
> >>> bigger than the packmol box when you tile the boxes, then equilibrate
> at
> >> constant
> >>> pressure to shrink the box, equilibrate the density, and arrange the
> box
> >> edges to be
> >>> consistent with periodic boundaries.
> >>>
> >>
> >> Let me make this less ambiguous.
> >>
> >> Your Packmol box is not the problem, the box assigned by LEaP is too
> small
> >> if it is
> >> the same as the Packmol box. Boxes created with packmol are not
> >> equilibrated with
> >> periodic boundaries. Packmol just puts packs spheres (connected spheres
> in
> >> the case
> >> of ethanol.) At the Packmol box boundaries, parts of molecules extend
> >> beyond the box.
> >> When the boxes are tiled with LEaP, some of the atoms overlap with the
> >> next image so
> >> you get VDW clashes. You need a LEaP box bigger than the packmol box
> when
> >> you tile
> >> the boxes, then equilibrate at constant pressure to shrink the PBC box,
> >> equilibrate
> >> the density, and arrange the PBC box edges to be consistent with
> periodic
> >> boundaries.
> >>
> >>> Good luck,
> >>> Bud Dodson
> >>>
> >>>> On Tue, Jul 23, 2013 at 10:02 AM, David A. Case <
> >> case.biomaps.rutgers.edu>wrote:
> >>>>
> >>>>> On Mon, Jul 22, 2013, Chinthaka Ratnaweera wrote:
> >>>>>>
> >>>>>> Once the saveoff command make a box 'unit' ( I guess I have to save
> >> it
> >>>>> as
> >>>>>> a lib file), inorder to use that unit to solvate the protein, do I
> >> have
> >>>>> to
> >>>>>> use loadoff command to open it and give this unit name as second
> >> argument
> >>>>>> in solvatebox command?
> >>>>>
> >>>>> Yes.
> >>>>>
> >>>>>>
> >>>>>> Does size of the solvate box matters when setup the initial box
> using
> >>>>>> packmol?
> >>>>>
> >>>>> It's not a big deal which size you choose. Most of the "standard"
> >> boxes
> >>>>> are really smaller than they should be (some were made back in the
> >> 1980s
> >>>>> when
> >>>>> computers were much slower.) The solvateBox and solvateOct routines
> >> will
> >>>>> replicate and truncate boxes as needed. Something on the order of
> 1000
> >>>>> ethanol molecules should be fine.
> >>>>>
> >>>>> ...good luck....dac
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Chinthaka Nadun Ratnaweera
> >>>> Hand Lab Rm 1126
> >>>> Mississippi State University
> >>>> 310 Presidents Circle
> >>>> Starkville, MS 39762
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> --
> >>> M. L. Dodson
> >>> Business email: activesitedynamics-at-gmail-dot-com
> >>> Personal email: mldodson-at-comcast-dot-net
> >>> Gmail: mlesterdodson-at-gmail-dot-com
> >>> Phone: eight_three_two-five_63-386_one
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> --
> >> M. L. Dodson
> >> Business email: activesitedynamics-at-gmail-dot-com
> >> Personal email: mldodson-at-comcast-dot-net
> >> Gmail: mlesterdodson-at-gmail-dot-com
> >> Phone: eight_three_two-five_63-386_one
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Chinthaka Nadun Ratnaweera
> > Hand Lab Rm 1126
> > Mississippi State University
> > 310 Presidents Circle
> > Starkville, MS 39762
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Tue Jul 23 2013 - 14:00:03 PDT
