THANKs sir its working
---------- Forwarded message ----------
From: Jason Swails <jason.swails.gmail.com>
Date: Tue, Jun 29, 2010 at 5:34 AM
Subject: Re: [AMBER] Fwd: how to allign the protein with average pdb
To: AMBER Mailing List <amber.ambermd.org>
Hello,
atomicfluct does NOT do an RMS fit. You must do that before with the rms
command. If you do not, then you will not get meaningful data. Also, it
does not make sense to RMS fit to each residue then see how it fluctuates
(it's doable, but meaningless). This is because you can easily fit 15 atoms
to a small RMS value over a trajectory, but the entire rest of the protein
may not align. You should align the backbone atoms with the rms command,
(using reference, like I put in my last email), then use atomicfluct.
Good luck!
Jason
On Mon, Jun 28, 2010 at 12:09 PM, REENU KHATTRI <ibi2008024.iiita.ac.in
>wrote:
> ---------- Forwarded message ----------
> From: REENU KHATTRI <lovelyshreen.gmail.com>
> Date: Mon, Jun 28, 2010 at 9:37 PM
> Subject: Re: [AMBER] how to allign the protein with average pdb
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> sir atomicfluct command does not take reference i checked the result many
> time but atomicfluct does not take reference b'coz the command is this
> atomicfluct out filename ...... byres
> between this line if i edit any thing it show segmentation fault
> so my problem is still same how to fit to reduce rmsd per residue wise not
> time wise
> plz help me.
> RINU KHATTRI
>
>
>
>
>
> On Mon, Jun 28, 2010 at 5:05 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > You need to load the average in as a reference, then use the "rms"
> command.
> > However, you need to use the "rms" command before you generate the
> average
> > structure, also.
> >
> > trajin trajectory.mdcrd
> >
> > rms first mass
> >
> > average avg.pdb pdb
> >
> > Then use that pdb as a reference:
> >
> > trajin trajectory.mdcrd
> > reference avg.pdb
> >
> > rms reference mass
> > atomicfluct _________ (I forget the exact usage).
> >
> > Good luck!
> > Jason
> >
> > On Mon, Jun 28, 2010 at 2:50 AM, REENU KHATTRI <ibi2008024.iiita.ac.in
> > >wrote:
> >
> > > hello sir i am calculating rmsd residue wise but result is not good i
> > want
> > > to first align or superimpose the protein with average pdb and use
this
> > > trajout file to perresidue wise calculation is any command to align a
> > > protein.
> > > RINU KHATTRI
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jun 29 2010 - 06:00:03 PDT
