Re: AMBER: MD & net charge

From: Carlos Simmerling <>
Date: Mon, 30 Aug 2004 09:23:20 -0400

parm99 is probably not a good choice for protein simulations.

Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>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.
>The AMBER Mail Reflector
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Received on Thu Sep 02 2004 - 01:15:12 PDT
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