AMBER Archive (2004)

Subject: Re: AMBER: MD & net charge

From: Chris Harrison (charris5_at_nd.edu)
Date: Mon Aug 30 2004 - 08:28:46 CDT

Could you please explain why parm99 is unsuitable for protein
simulations and if so, what forcefield would be suitable for protein
simulations?

Chris
charris5_at_nd.edu

Carlos Simmerling wrote:

> 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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