Hello Daniel
Yes it indeed clears up quite a lot of confusion happening at my end.
Sorry for the trouble and thanks a lot for the elaborate explanation.
Regards
From: Daniel Roe<mailto:daniel.r.roe.gmail.com>
Sent: 29 June 2020 20:35
Cc: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Ligand movement w.r.t protein backbone
Hi,
A broad question like "what is the difference in outputs?" is really
difficult to answer. I really recommend reading the manual entries for
the commands and keywords you are using. Also make sure you read
through the output cpptraj gives, at least the first time you do the
calculation. The output isn't perfect, but cpptraj tries to tell you
exactly what it's doing and any issues it might be encountering.
On Mon, Jun 29, 2020 at 12:24 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> rms reference mass out backbond_aligned_RMSD.txt :3-286.CA,C,N,O
This is calculating the mass-weighted coordinate RMSD of atoms
selected by your mask (residues 3 to 286, atoms CA, C, N, and O) in
your target to those atoms selected in your reference structure;
fitting (optimal translation/rotation to line up the selected atoms as
best as possible) is done by default.
>
> rms IPA_site1 :IPA&!.H= nofit mass out lig_probb_rmsd.txt
This is calculating the mass-weighted coordinate RMSD of atoms
selected by your mask (residue IPA, no atoms beginning with H) in your
target to those atoms selected in your reference structure; no fitting
is done, so the RMSD is with respect to the previous RMSD command
(i.e. backbone of residues 3 to 286). In other words it will reflect
the translation/rotation of the ligand in the reference frame of the
protein backbone.
Hopefully this clears things up a bit.
-Dan
>
> go
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> From: Daniel Roe
> Sent: 29 June 2020 12:07
> To: AMBER Mailing List
> Subject: Re: [AMBER] Ligand movement w.r.t protein backbone
>
>
>
> Hi,
>
> On Sat, Jun 27, 2020 at 5:29 AM Prasanth G, Research Scholar
> <prasanthghanta.sssihl.edu.in> wrote:
> >
> > Dear all,
> > I would like to compute the RMSD of ligand w.r.t the backbone of protein
> > during the simulation. Can you please suggest if this cpptraj script will
> > give me the intended result
>
> Not exactly; this will just give the RMSD with respect to the ligands
> position in the first frame. You should first fit on the protein, then
> do 'nofit' RMSD on the ligand (so that it's actually calculated in the
> reference frame of the protein). So e.g. (assuming your protein is
> molecule 1):
>
> rms Protein ^1.C,CA,N mass
> rms rms1 :LIG&!.H= nofit mass out results/lig_probb_rmsd.dat
>
> Hope this helps,
>
> -Dan
>
> > --
> > parm comdry.prmtop
> > trajin production_no_wat_ions.nc
> > rmsd rms1 ":LIG&!(.H=)" nofit mass out results/lig_probb_rmsd.dat
> > go
> > clear all
> > quit
> > --
> > I felt this script gives the rmsd of ligand w.r.t protein. Can you please
> > suggest a solution.
> > Thank you.
> > --
> > Regards,
> > Prasanth.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
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Received on Tue Jun 30 2020 - 05:30:03 PDT
