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
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
Received on Tue Jul 23 2013 - 13:30:03 PDT
