[AMBER] Best method to calculate vdW energies between residue side chains

From: Intravaia, Lauren E via AMBER <amber.ambermd.org>
Date: Mon, 13 Jan 2025 20:23:59 +0000

Hello,

I am trying to calculate the vdW energy of side chains between residues 1 and 2 throughout the MD trajectory. The command I am using now is pairwise through cpptraj:

pairwise :1,2&!(.N,CA,C,O,H*) out pair_1_2.dat

Is this the best method to calculate pairwise interactions?

Thanks in advance,
Lauren Intravaia

--
Lauren Intravaia
PhD Candidate
Celia Schiffer Lab
Dept. of Biochemistry and Molecular Biotechnology
University of Massachusetts Chan Medical School
364 Plantation St. LRB 970D
Email: lauren.intravaia.umassmed.edu<mailto:lauren.intravaia.umassmed.edu>
LinkedIn: www.linkedin.com/in/lauren-intravaia<http://www.linkedin.com/in/lauren-intravaia>
Lab website: https://www.umassmed.edu/schifferlab/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jan 13 2025 - 12:30:03 PST