AMBER Archive (2004)

Subject: Re: AMBER: MD & net charge

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Aug 30 2004 - 08:41:21 CDT

we and others have published articles showing that parm99
strongly overstabilizes alpha-helical conformations. on the ns-timescale
things may be ok, but over longer periods the protein becomes
more helical. folding studies with parm99 are likely worthless.

there are several parm94 variants that have been published in the past
few years. we published a change in 2002, Angel Garcia uses a
different modification, and so on. AMBER8 includes a few of these.
carlos

===================================================================
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
===================================================================

Chris Harrison wrote:

> 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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>
>
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