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
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Received on Mon Dec 03 2012 - 06:30:02 PST
