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
> > >
> >
> >
> > ______________________________________________________________________
> > सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> > Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> > सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> > पिन कोड/PIN CODE :160036
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> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Mon Dec 03 2012 - 07:00:02 PST
