Haining, you'll need to decide what atoms of your ligands are truly
correspondent, first. Having ligands that are similar doesn't guarantee
you an rmsd--for practical purposes in cpptraj, ligand RMSD is defined for
structures with identical compositions. After you have the list of
equivalent atoms, you'll need to ask yourself what reference frame you
want. Do you just care about the overall shape of the ligand (if you have
two big and floppy ligands, I can see some value in this)? If that's the
case, then the reference frame is something defined for the ligands
only--you align one ligand to the other by the equivalent atoms you have
chosen, for each frame of the trajectory, find the best superposition you
can get, then add up the squared distances between the pairs of equivalent
atoms and take the square root of the sum (root mean squared deviation).
Or, do you want to know where the two ligands sit relative to one another
in the reference frame of the receptor protein (this may be more up your
alley)? If that's the case, then for each frame of the simulation, you
need to define the protein and ligand as a single rigid body, align the
protein (backbone) atoms, and then compute the RMSD for ligand equivalent
atoms. cpptraj has some things to do this (see rmsd2, for example), but
again you need to take care of the ligand non-congruence first.
I'd recommend the following:
- Decide on your equivalent atoms
- Print your trajectories in .crd format
- Write a homemade python script to dissect the list of coordinates
- Rearrange, clip, or add zeros to the second trajectory as necessary
to get all of the coordinates in the second trajectory to line up in order
with the first, so that equivalent atoms appear in the same order.
- Read both trajectories according to the topology of the first--you'd
get horrible energies for he second trajectory but that's not what cpptraj
cares about.
- Use cpptraj features to give you the rmsd you seek.
HTH,
Dave
On Mon, Nov 28, 2016 at 4:32 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> 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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> > AMBER.ambermd.org
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
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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 - 14:00:04 PST
