AMBER Archive (2004)

Subject: Re: AMBER: MD & net charge

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Aug 30 2004 - 08:23:20 CDT

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: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

bybaker_at_itsa.ucsf.edu 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.
>
>Bo
>
>
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