Dear Dr. Jason Swails and amber community member,
Thanks for that suggestion and inputs.
I have tried the following changes in the input where I have aligned all of
the backbone residues and used the atomicfluct command. But the b factors in
the output files have very small values (0-60) than the expected and are
almost same for four set of protein-ligand complexes I'm studying. They are
expected to show some difference as per the available literature on the
same.
Please suggest what changes I should make to the input so as to plot
fluctuations in the backbone of the H-12 helix (residue 259-271). How can I
get residue wise rmsd on the y-axis and residue no. on x-axis in the plot?
This way I will be able to show that backbone rmsd for selected residues is
more in some cases and less in other.
Thanks once again and waiting for your valuable comments and suggestions...
The input file for ptraj is as follows:
-----------
trajin 2PRG_pio_1nsmd.mdcrd
center :1-284
image origin center
strip :WAT
rms first out 2PRG_pio_1nsMD_prak_1.rms .N,C,CA
atomicfluct out 2PRG_pio_1nsMD_prak_1.apf :259-271.N,C,CA byres bfactor
EOF
------------
On 7/12/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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
>
--
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
Received on Mon Jul 12 2010 - 09:30:06 PDT
