That synrax chooses everything in those residue numbers except hydrogen.
So it will work for your glycoprotein.
However,be sure that this is what you want to do. For example, the glycan
posirions are often not well defined in experiment, so defining an accurate
reference position may not be possible.
On Thu, Aug 25, 2022, 2:03 AM Sayan Poddar via AMBER <amber.ambermd.org>
wrote:
> Dear AMBER developers and Users,
>
> I am trying to calculate the RMSD of a glycoprotein molecule through
> cpptraj.
> I have used the syntax *rms rmsd_fep1 reference out rmsd_prot.dat
> :1-428.N,C,CA* and
> *rms rmsd_fep2 reference out
> rmsd_gly.dat :429-453&!.H=*
> for separately calculating the protein (for backbone atoms) and glycan (all
> atoms excluding hydrogens) RMSD, respectively.
>
> Initially, I used the syntax *rms rmsd_fep3 reference out rmsd_glyco.dat
> :1-428.N,C,CA,429-453&!.H= *for calculating the combined RMSD of the
> glycoprotein but after plotting, its RMSD is showing only the protein RMSD.
> Hence I have used the syntax
> *rms rmsd_fep3 reference out rmsd_glyco.dat :1-453&!.H= *for the
> calculation.
>
> So my query is, is the syntax *rms rmsd_fep3 reference out rmsd_glyco.dat
> :1-453&!.H=* correct for calculating the combined RMSD of the complex
> consisting of both protein and glycans?
>
> Thank you
>
> *with regards*
> *Sayan Poddar*
>
> *PhD Research Scholar*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology Indore*
> *India*
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>
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Received on Thu Aug 25 2022 - 03:30:03 PDT
