AMBER Archive (2008)

Subject: AMBER: query about Generalized Born simulation

From: gurvisha_at_leadinvent.com
Date: Fri Apr 11 2008 - 08:42:23 CDT

Dear Amber users

I am trying to run an implicit GB simulation for protein-DNA complex using
amber9. My doubt is whether PME can be turned on for an implicit GB
simulation. Although the Amber9 manual states that Generalized Born
simulations can only be run for non-periodic systems, i.e. where ntb=0, it
also mentions that the nonbonded cutoff for GB calculations should be
greater than that for PME calculations. So can PME be used for a GB
simulation?

Regards
Gurvisha Sehgal

LeadInvent Technologies
Technology Business Incubation Unit(TBIU)
IIT Delhi
Hauz Khas, New Delhi 110 016
INDIA.

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