thank you very much sir for the suggestions
On Tue, Jul 2, 2013 at 10:02 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Jul 1, 2013 at 8:01 PM, Mary Varughese
> <maryvj1985.gmail.com<javascript:;>>
> wrote:
> > i am used to center and image commands in ptraj for reimaging . should i
> > switch to autoimage of cpptraj?
>
> This is what I would recommend. The 'autoimage' command was designed to be
> easier to use.
>
> > could u please explain about wrapping artifacts. how can i check it, just
> > visualize?
>
> Either that, or an artifact will typically show up as a large spike in an
> RMSD calculation.
>
> > Also sir, on doing rms first mass of a dna ligand system;
> > rms first mass :1-24.P,O3',O5',C3',C4',C5' time 1.0
> > does this command take care of my ligand :25 also.
>
> No. ":1-24" literally means "residues 1 to 24". One thing you can do to see
> how residue 25 moves with respect to residues 1-24 is use that initial mask
> to perform the initial fit, then do an rms calculation on residue 25
> without
> fitting, e.g.:
>
> rms first mass :1-24
> rms first mass :25 nofit out rms.25.dat
>
> -Dan
>
> > or should i use
> > rms first mass :1-24.P,O3',O5',C3',C4',C5' :25 time 1.0
> > but this command output says nothing about :25
> > how can i now ligand is also rms fitted?
> >
> >
> > On Tue, Jul 2, 2013 at 7:08 AM, David A Case <case.biomaps.rutgers.edu
> <javascript:;>
> >wrote:
> >
> >> On Mon, Jul 01, 2013, Mary Varughese wrote:
> >> >
> >> > in the production dynamics(in NPT):
> >> > when ntb=2, ntp=1, pres0=1.0, ntt=3
> >> >
> >> > 1: what should be the appropriate value of gamma_ln ? (i have used 1 )
> >> > does increasing value to 5.0 has any advantage
> >>
> >> I doubt that you could see any difference between 1 and 5.
> >>
> >> > 2: also what is the significance of taup=2.0 ; how does it affect the
> >> > dynamics
> >>
> >> The affects the speed at which the volume of the system responds to
> >> pressure
> >> fluctuations, and hence to the magnitude of the fluctuations themselves.
> >> If your system is too small (doesn't have enough water molecules) the
> >> value
> >> of this variable might cause a noticeable difference, although I have
> not
> >> personally seen such a case.
> >>
> >> > 3: also should i essentiallly include ig=-1 as it says in amber DNA
> >> > tutorials in the case of ntt=3.
> >>
> >> Yes: this is essential.
> >>
> >> > 4: Also i hope adding these values doesnt affect mmpbsa calculations.
> >>
> >> Not setting ig=-1 could lead to very bad results. Minor variations in
> >> gamma_ln or taup are unlikely to have measurable effets.
> >>
> >> >
> >> > 5: Also sir does iwrap=1 has any influence on mmpbsa calculations?
> >>
> >> It can. The safest course of action is to use the "autoimage" command
> in
> >> cpptraj before handing things off to mm-pbsa. Also, be sure to
> visualize
> >> your trajectory (after autoimage) to make sure there are no wrapping
> >> artifacts.
> >>
> >> ...dac
> >>
> >> p.s.: be sure to study reviews of mm-pbsa calculations, and look for
> >> papers that report calculations similar to the ones you are planning.
> In
> >> my opinion, a careful study of what happens during your simulation is a
> >> lot more likely to lead to new insights than are the energies that come
> >> out of the mmpbsa analysis.
> >>
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 01 2013 - 22:00:05 PDT
