[AMBER] Query regarding glycoprotein RMSD calculation

From: Sayan Poddar via AMBER <amber.ambermd.org>
Date: Thu, 25 Aug 2022 12:32:33 +0530

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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Received on Thu Aug 25 2022 - 00:30:03 PDT
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