From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Wed Nov 06 2013 - 13:58:57 CST
Hi Kenno,
Yes it is top_all35_ethers.rtf and par_all35_ethers.prm. Thanks for
clarification.
I noticed there is existing work using these parameters for PEGylated
lipids and micelles. However, I did not find existing work for simulating
PEG with protein. Your response was helpful to carry out the work with some
confidence. I will look into verification of the results with experimental
data.
Regards,
Roy
On Wed, Nov 6, 2013 at 2:27 PM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:
> - I know of no top_all35_ethers-oh.rtx file; to be safe, it's probably
> best to use top_all35_ethers.rtf and par_all35_ethers.prm from the official
> force field distribution.
>
> - There is a large body of evidence suggesting that the (mostly
> water-oriented) CHARMM parameter optimization procedure yields relatively
> well-balanced interactions between different CHARMM solutes (eg. protein
> and a PEG chain) in TIP3P water (except for ions, which sometimes require
> NBFIX terms). Therefore, I would expect the PEG parameters to be
> appropriate for your purpose. It never hurts to verify against experimental
> data that is directly relevant to your project, though.
>
>
>
>
> On 11/06/2013 01:21 PM, Roy Fernando wrote:
>
>> Hello NAMD experts
>>
>> I plan to run a protein simulation with Polyethylene Glycol (PEG).
>>
>> I notice that there exist CHARMM force filed parameters for PEG
>> (top_all35_ethers-oh.rtx). from previous work (Vorobyov et al. 2007 and
>> Lee et al 2008). However, those parameter are developed for PEG
>> interaction with water.
>>
>> I wonder if these parameters are still good for equilibrating protein with
>> PEG?
>>
>> Thanks a lot , in advance.
>>
>> Roy
>>
>
>
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