[AMBER] Calculating RMSD between apoprotein and protein-ligand complex

From: Alexander Hung Lee via AMBER <amber.ambermd.org>
Date: Sat, 3 Feb 2024 01:18:38 +0000

Hello,

I ran a 1us md of the apoprotein and want to compare 2 specific residues with that of the ligand-bound version of it. I deleted the ligand from the reference. Because they're sourced from 2 different crystal structures, they don't have the same # of residues. I was following this tutorial for RMSD use with different topologies https://ambermd.org/tutorials/analysis/tutorial1/index.php and this is what I have so far... I don't know if I'm doing this correctly?

parm apo.pdb
trajin apo.nc
parm reference.pdb
reference reference.pdb parm reference.pdb [reference]
rms ref [reference] :2-136.CA :1-135.CA
rms ref [reference] :118 :117 out GLN.txt nofit
rms ref [reference] :3 :2 out TYR.txt nofit
run


Residue #
PDB
Same
Residue of
Interest 1
Residue of
Interest 2
Apo
2 - 136
118
3
Reference
1 - 135
117
2


[https://res-h3.public.cdn.office.net/assets/mail/file-icon/png/zip_16x16.png]System 1.zip<https://outlookuga-my.sharepoint.com/:u:/g/personal/ahl63010_uga_edu/EdXx1GH5WlRAueBxtZRFnZAB_VSkA69KsV5-RP5bAKwhWQ>,

Thank you,
Alex Lee
PhD Student
Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/>
Department of Biochemistry & Molecular Biology
Complex Carbohydrate Research Center
University of Georgia

315 Riverbend Rd.
Athens, GA 30602
Email: ahl63010.uga.edu
Mobile: (470) 641-3884
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Received on Fri Feb 02 2024 - 17:30:02 PST