Hello,
I was going to suggest atomicfluct. However, I'd suggest that you align to
the whole backbone, not just 2 residues. By only RMS fitting to only a
couple residues, your fluctuations may appear artificially small.
Hope this helps,
Jason
On Mon, Jul 12, 2010 at 9:57 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> Dear Dr. Daniel Roe and amber community members,
> Thanks for that suggestion.
> Actually what I want is like this:
> I want to process the trajectories such that on x-axis I want residue
> number
> say 259-271 and on y-axis rms (0.0 to 1.0).
> I'm not sure what you suggested will give me that result.
> Currently I'm using the following input structure that is giving me residue
> no. on x-axis but not the rms on y-axis.
> Please find time and see if you can suggest some changes that will give me
> the desired plot.
>
> ---------
> trajin rosi_MD_equil.mdcrd
> trajin rosi_MD_1ns.mdcrd
> center :1-271
> image origin center
> strip :WAT
> rms first out rosi_MD_prak.rms :259-271.N,C,CA
> atomicfluct out rosi_MD_park.apf :259-271.N,C,CA byres bfactor
> EOF
> ------
>
>
> On 7/12/10, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Woops, I actually forgot the 'nofit' option...what I meant was:
> >
> > rms first out RMSD_Res10.dat :10 nofit
> >
> >
> > On Mon, Jul 12, 2010 at 9:47 AM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > > Once you have fit your coordinates to the desired reference frame you
> > > can get the RMSD of specific residues within that frame by using
> > > additional RMS commands with the 'nofit' option, e.g.:
> > >
> > > rms first out RMSD_Res10.dat :10
> > >
> > > On Mon, Jul 12, 2010 at 4:30 AM, vaibhav dixit <
> vaibhavadixit.gmail.com>
> > wrote:
> > >> Dear Amber community member,
> > >> I have performed 1ns MDS on protein-ligand complexes. Now I'm
> interested
> > to
> > >> know the rmsd residue wise fluctuation for each complex which I can
> plot
> > >> using xmgrace and show that a few ligands stabilizes H-12 helix while
> > others
> > >> don't.
> > >>
> > >> For this I'm using the following input file for ptraj with the command
> > >>
> > >> $AMBER/exe/ptraj 2PRG_rosi.prmtop < rosi_MD_backboneAF2.in
> > >>
> > >> rosi_MD_backboneAF2.in
> > >> ------------------------------------------------
> > >> trajin rosi_MD_equil.mdcrd
> > >> trajin rosi_MD_1ns.mdcrd
> > >> rms first out rosi_MD_backboneAF2.rms :259-271.N,C,CA
> > >> -----------------------------------------------------
> > >> The command runs successfully and generates the file
> > rosi_MD_backboneAF2.rms
> > >> (file attached), but when I plot using xmgrace it gives 800 point on
> the
> > >> x-axis instead of AA number i.e. 259 to 271.
> > >>
> > >> Please suggest the necessary modification so that I can actually get
> the
> > >> residue wise rmsd which I can compare for different ligands.
> > >> Waiting for your response and help...
> > >> Thanks in advance...
> > >>
> > >> --
> > >> 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
> > >>
> > >>
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe
> > > Postdoctoral Associate
> > > SAS - Chemistry & Chemical Biology
> > > 610 Taylor Road
> > > Piscataway, NJ 08854
> > >
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Postdoctoral Associate
> > SAS - Chemistry & Chemical Biology
> > 610 Taylor Road
> > Piscataway, NJ 08854
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 12 2010 - 07:30:03 PDT
