---------- 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
>
>
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Received on Mon Jun 28 2010 - 09:30:03 PDT
