Currently, I have these commands to calculate the closest 5: SIA out of 45 floating to a binding site each frame
parm ../2_md/CPLX_Neut_Sol.parm7
trajin ../2_md/10.1.produ.nc
rms :1-1469 first # align receptor
closest 5 :132-134 solventmask :SIA closestout SIA2ChainA_Binding_sites.dat name SIA
run
exit
The output file contains
Frame Molecule Distance FirstAtom#
which to my understanding, the distance is from the :SIA atom closest to the enter of mass of the residues :132-134
1.
Is there some way to do the distance from center of mass :SIA to center of mass residues instead?
Ex: [distance of closest :SIA atom to residues ] > [distance of :SIA center of mass to residues]
2.
Is there a way to do RMSD calculation of those selected molecules to a pdb reference? I was thinking along the lines of "for FRAME in" maybe?
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 Mon Jul 15 2024 - 11:30:01 PDT
