Hii Dan
Thank you. Now I have got a way. Thank you very much
sanjib
On Tue, Aug 28, 2012 at 9:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Aug 28, 2012 at 9:33 AM, Sanjib Paul <sanjib88paul.gmail.com>
> wrote:
> > Actually
> > I want a starting structure for nmode analysis which would have very
> small
> > root-mean-square gradient. I thought after getting a average structure I
> > would minimiza it and then that minimized structure would be starting
> > structure.
>
> But once you minimize the averaged structure you'll end up with
> something different anyway. Averaged structures can be useful as
> references for rmsd etc but not much good as a starting structure. Why
> not just take the lowest energy structure from your trajectory and
> minimize that, or alternatively minimize all of the structures from
> your trajectory using an imin=5 run and take the lowest E structure
> from that?
>
> -Dan
>
> >
> > Sanjib
> >
> > On Tue, Aug 28, 2012 at 7:43 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> On Tue, Aug 28, 2012 at 10:05 AM, Sanjib Paul <sanjib88paul.gmail.com
> >> >wrote:
> >>
> >> > Dear Amber Users,
> >> > I wanted to generate a average structure
> >> form 1
> >> > ns trajectory file of my protein using 'average' command of ptraj. My
> >> input
> >> > file is like following:
> >> > trajin protein_prod_1ns.mdcrd
> >> > average protein_prod_1ns_avg.pdb pdb
> >> >
> >>
> >> Note, the 'average' command does not do any kind of implicit fitting, so
> >> you are including free rotation and translation in your average (which
> is
> >> *NOT* something you probably want to do).
> >>
> >> To get rid of these contributions, add a "rms" command before 'average'.
> >>
> >>
> >> > When I observe my pdb file of average structure I noticed that some
> >> portion
> >> > of protein is very unstable and very absurd. Atoms are overlapping and
> >> some
> >> > unusual bonds are also present. Then, I followed analysis portion of
> >> > TUTORIAL B3. Here also structure is like before. Some unusual bonds
> and
> >> > overlapped atoms are present. How can I overcome it? Please help.
> >> >
> >>
> >> 'Warped' and 'strange' structures are expected for an average (to some
> >> extent). Consider for instance a freely rotating methyl group such that
> >> all hydrogens attached to the CH3 are rotationally degenerate. In this
> >> case, each hydrogen atom should have the *same* average coordinates
> which
> >> should lie almost directly on top of the C atom they are all attached
> to.
> >>
> >> You should think about what you really want and whether or not an
> 'average'
> >> structure satisfies your needs.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
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> >>
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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)
>
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Received on Tue Aug 28 2012 - 10:00:03 PDT
