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
Received on Mon Jul 12 2010 - 07:00:09 PDT
