AMBER Archive (2004)

Subject: Re: AMBER: MD & net charge

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Aug 30 2004 - 15:57:50 CDT

you can get just the force field files from
http://amber.scripps.edu/dbase.html

whether you should allow PME to use a neutralizing plasma or add counterions
doesn't have a definite answer (yet). some people argue for each approach.
ions are more accurate in principle but take time to equilibrate, and
without
equilibration they may be worse than not having them at all. it's really
an area of
current research.

bybaker_at_itsa.ucsf.edu wrote:

>Thanks for the advice.
>
>Since we only have Amber7 available, I might have to use the old parm94.
>
>Do I still need to neutralize the entire system before subject to MD?
>
>Thank you.
>
>Bo
>
>
>
>On Mon, 30 Aug 2004 09:41:21 -0400 Carlos Simmerling wrote:
>
>
>
>>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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