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
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Received on Mon Jul 12 2010 - 07:00:06 PDT
