Dear All,
I want to understand how ions (Na, K and Cl) are distributed around a
ligand during the MD simulation and if there are differences between two
simulations.
I have used the contacts command in cpptraj (like the following) which
gives me the min and max distances in each frame between the ions and
residue 614.
My question is how to get more of a statistical analysis of the
distribution of ions around the cofactor. Can I use the closest command to
get what I want here? if yes, what options I should use?
Please do give your valuable suggestions.
nativecontacts name cofac-K :614&!.H= :K+ byresidue out cofac-Kcontacts.dat
mindist maxdist distance 10.0 first map mapout cofac-Kresmap.gnu contactpdb
cofac-Kcontactmap.p
db series seriesout cofac-Knativecontacts.dat writecontacts
cofac-Kwritecontacts.dat
Thank you and best regards.
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Thu Nov 25 2021 - 01:30:01 PST
