AMBER Archive (2004)

Subject: AMBER: MD & net charge

From: bybaker_at_itsa.ucsf.edu
Date: Sun Aug 29 2004 - 01:19:18 CDT

Hello, Amber:

I am planning to run MD on my protein structure model under physiological
(pH 7.0) and acidic (i.e. pH 4.0) conditions. In order to mimic the low
pH condition, all Asp, Glu and His residues in the model will be changed
to their protonated states. After the changes, the net charge of the
structure is +32. Should I neutralize the structure by ‘addIon2’ before
any energy minimizations, or just leave it without adding Cl- ions ?

I use Amber7 with ff.99 force field.

Thanks advance.

Bo

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