From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Nov 06 2013 - 13:27:41 CST
- 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
> Thanks a lot , in advance.
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