[AMBER] Using the rep.C0.pdb as a reference structure in RMSD analysis

From: Soheila Shokrollahzade <soheilashokrollahzade.gmail.com>
Date: Tue, 24 Nov 2020 10:56:42 -0500

Hi Daniel,

I ran MD simulation of wild type insulin at first and then I muted one of
the residues and ran MD on the new structure calling it model1. So we have
wild type (WT) and model 1 (mod1). I ran dbscan clustering on WT using an
epsilon of 1 Å. After finishing the analysis I have rep.c0.pdb as the most
dominant cluster of WT. I wanted to use rep.c0.pdb as a reference structure
on which mod1 can be fitted when running RMSD. I ran the following script
but it seems like that it doesn’t take rep.c0.pdb. Would you please help me
figure out how can I fit the trajectory of model 1 on the most dominant
cluster of WT?

parm out.top
trajin mode-1.nc
reference rep.c0.pdb [c0]
rms RMSD ref [c0]
rms RMSD .CA,C,N,O out c0.txt
rms FIT @CA,C,N,O to-reference.txt

Thank you,

*PhD student of Biomedical Engineering, Garton lab
*Institute of Biomedical Engineering (BME) *
*University of Toronto*
*Room 422, Rosebrugh building, 164 College Street, Toronto, ON, M5S 3E2*
AMBER mailing list
Received on Tue Nov 24 2020 - 08:00:02 PST
Custom Search