that will not do it.
AT, please re-read what
Haining Liu was aking
The request is for rmsd between trajs at EACH frame for both, and your
script would just get you RMSD vs time for ONE trahectory vs its first
frame.
adrian
On 11/28/16 2:27 PM, Thakur, Abhishek wrote:
> You can use cpptraj to do RMSD by following the script
>
>
> Make a trajin file
>
> trajin X.crd.gz
> strip :WAT
> strip :Ions
> rms first out X_RMSD.out time 0.005 :residue range
>
>
> cpptraj X.prmtop < X.trajin > Y.out
>
>
>
> with regards,
>
> AT
>
> ________________________________
> From: Haining Liu <Haining.Liu.175.nd.edu>
> Sent: Monday, November 28, 2016 9:49:02 AM
> To: AMBER Mailing List
> Subject: [AMBER] RMSD for two different MDs
>
> Hi Amber list,
>
> I want to compare the RMSD of two different ligands in the same protein to
> find out whether they have similar binding. Specifically, I have
>
> protein + ligand 1 (50 ns MD)
> protein + ligand 2 (50 ns MD)
>
> ligand 1 and ligand 2 structurally different, but similar. I want to get
> the RMSD of ligand 1 and ligand 2 in each of the 50 ns snapshot. Is there a
> way to do this by cpptraj?
>
> Thank you very much for your help.
>
> Haining
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Nov 28 2016 - 14:00:03 PST
