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
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Received on Mon Jul 12 2010 - 07:00:05 PDT
