AMBER Archive (2005)

Subject: AMBER: why not minimize snapshots before MM/PBSA calculations

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Tue Jul 26 2005 - 10:02:00 CDT


Dear AMBER Users:

If there's only one snapshot when performing MM/PBSA calculation for the
binding free energy, I think it's necessary to minimize the structure to
local minimum to obtain the lowest energy. However, when there's a MD
trajectory for one to evaluate the binding free energy, no
energy-minimization will be performed for MM,GB, and PB calculations. My
question is, why not minimize the snapshots until convergence before
MM,GB,PB,NM calculations? Thanks in advance!

Best Regards!

Liu

-- 
JunJun Liu

College of Chemistry Central China Normal University WuHan 430079 P.R. China ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu