Dear Amber People,
I have two related questions concerning GB that I hope you could kindly
answer or address.
1.If we have a modified residue, does this modified residue need some
special GB parametrization in addition to the routine parametrization
(such as resp calculation, prepin file preparation) if we were to run GB?
2. We have run into cases where a GB protocol would hang (due to extremely
high energy ******) while a dielectric function protocol could proceed.
This took place in the initial minimization (which means the starting
structure are exactly the same while the selection of GB or dielectric
function was the only difference). Do you have any comments on this?
Thanks in advance for your input.
Lihua
On Mon, 11 Apr 2005, Carlos Simmerling wrote:
> Date: Mon, 11 Apr 2005 09:18:07 -0400
> From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
> Reply-To: amber.scripps.edu
> To: amber.scripps.edu
> Subject: Re: AMBER: Two question about dielectric constant
>
> I think that opinion has changed over time and now most people
> would recommend use of GB solvation instead of a distance dependent
> dielectric. this avoids (at least mostly) both of the points you raise
> below.
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate 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.stonybrook.edu
> ===================================================================
>
>
>
>
> 烨 武 wrote:
>
>> I'm sorry to ask questions again which may be asked frequently.
>> I have read some letters about this items in the archive, but I am
>> still confused about these questions, so please help!
>> I want to minimize a structure of a protein considering the solvent
>> effects but excluding explicit water.
>> In the Frequently Asked Questions
>> (FAQ)("http://amber.ch.ic.ac.uk/Questions/dielc.html), it said:
>> "In the case of excluding explicit water the distance dielectric model
>> seems to be the most fashionable,------"
>> But I still have two question:
>> 1.In this situation, when we use the distance dielectric model, which
>> value should we choose for dielectric constant, 1 or larger,in order
>> to model the water surrounding better?
>> 2. In above distance dependent dielectric setting, will the software
>> use the same dielectric constant value when computing the
>> electrostatic interactions between two atoms separated by other
>> protein atoms and two atoms seperated by surrounding waters (if the
>> distance is the same)?
>> If it is true, I think it is unreasonable, itn't it?
>> Thank you for your help!
>> Zheng Canhui
>>
>>
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>
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Received on Mon Apr 11 2005 - 18:53:00 PDT
