Re: [AMBER] rmsd of trajectories with different no. of residues in same protein?

From: Vaibhav Dixit <vaibhavadixit.gmail.com> Date: Mon, 3 Dec 2012 22:26:14 +0530 · > [trajin

--
On Mon, Dec 3, 2012 at 8:23 PM, Jason Swails <jason.swails.gmail.com> wrote:
> cpptraj was designed specifically for this task.  You can load structures
> with different topologies and calculate RMSDs between 'different'
> structures (as long as the selection in both structures have the same # of
> atoms).
>
> Look at the manual for cpptraj to learn how to use it.
>
> Good luck,
> Jason
>
> On Mon, Dec 3, 2012 at 9:25 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Monica,
> > Waters and ions are already removed from the trajectory, so they are not
> > the source of problem here.
> > I must emphasize that, I want to plot rmsd for the trajectory with
> > reference to a structure (PDB) which has one residue less than those
> > present in the MD trajectory.
> > This is causing ptraj warning for mismatch in number of atoms.
> >
> > On Mon, Dec 3, 2012 at 6:02 PM, <monica.imtech.res.in> wrote:
> >
> > > Hi
> > >  I guess ypu can remove water and other ions etc.from the prmtop file
> and
> > > then
> > > try one more time for rmsd calculation by ptraj coz atom number
> > difference
> > > can
> > > be due to this.
> > >
> > > Thanx
> > > monica
> > >
> > >
> > > > Dear Amber community members,
> > > > I have trajectory files for a protein generated from different PDB
> > files
> > > > with different number of residues.
> > > > For e.g. I have structure 1PRG with residues 1-270 and 2PRG with
> > residues
> > > > 1-271 (272 is ligand).
> > > >
> > > > Now I want to plot rmsd between trajectory of 2PRG and reference
> > > structure
> > > > (PDB generate with ambpdb) of 1PRG.
> > > > I am following the below mentioned procedure, but I'm not sure if the
> > > > results are meaningful (rmsd > 500 ?).  Ptraj also gives warning that
> > > > expected and actual number of atoms are different.
> > > >
> > > > *Please suggest me how can I use two prmtop for different
> trajectories
> > > > together to get the rmsd between two trajectories of same protein but
> > > with
> > > > different number of residues (hence different sequence).*
> > > >
> > > > Step 1. ptraj 2PRG.prmtop < 2PRG_new_traj.in
> > > >
> > > > ptraj input file for step 1.
> > > > 2PRG_new_traj.in
> > > > ------------
> > > > trajin 2PRG.mdcrd
> > > > strip :271
> > > > trajout 2PRG_new.mdcrd
> > > > -----------
> > > >
> > > > Step 2. Then I have generated prmtop for 2PRG with residue 271
> deleted
> > > > (2PRG_new.prmtop)
> > > >
> > > > Step 3. ptraj 2PRG_new.prmtop < 2PRG_1PRG.in
> > > >
> > > > ptraj input file for step 3.
> > > > 2PRG_1PRG.in
> > > > ---------
> > > > trajin 2PRG_new.mdcrd
> > > > rms reference 1PRG.pdb out 2PRG_1PRG.rmsd :1-271.CA,C,N,O
> > > > --------
> > > >
> > > >
> > > > --
> > > > With regards
> > > >
> > > > Vaibhav A. Dixit
> > > > Ph.D. Scholar
> > > > Department of Medicinal Chemistry
> > > > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > > > Sector 67, Phase X,  S.A.S. Nagar (Mohali)
> > > > Punjab -160 062 INDIA
> > > > Phone (Mobile): +919915214408
> > > > E-mail: vaibhavadixit.gmail.com
> > > > www.niper.nic.in
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > ______________________________________________________________________
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> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X,  S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
-- 
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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