Subject: Discussion group for the ARIA software
List archive
- From: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>
- To: "aria-discuss AT services.cnrs.fr" <aria-discuss AT services.cnrs.fr>
- Cc: Benjamin Bardiaux <bardiaux AT pasteur.fr>, "Roe, Leah" <Leah.Roe AT ucsf.edu>
- Subject: Re: [aria-discuss] ARIA Calculation Larger Protein
- Date: Wed, 5 Aug 2020 17:32:37 +0000
- Accept-language: en-US
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Hello everyone,
we are trying to calculate the structure of a moderately largish protein (167 aa) using Aria. Our 1st couple of runs using the ‘Standard Protocol’ (20 structures per iteration and the normal number of steps) do not look like they are converging
(see values from the report file it0…it8 & refine below). I remember some papers say the number of steps should be increased for larger proteins. Should we start with the parameters from Mareuil et al., 2015? Should we use the log-harmonic potential right
from the start or should we only turn that on once we have identified what we think are the larger violations?
stay safe and take care,
Mark
All Atoms:
## Backbone (N,CA,C,O) : 10.44 +/- 1.03 A
## Backbone (N,CA,C,O) : 9.56 +/- 1.07 A
## Backbone (N,CA,C,O) : 10.60 +/- 1.58 A
## Backbone (N,CA,C,O) : 10.74 +/- 1.59 A
## Backbone (N,CA,C,O) : 11.91 +/- 1.44 A
## Backbone (N,CA,C,O) : 12.15 +/- 2.64 A
## Backbone (N,CA,C,O) : 13.28 +/- 5.84 A
## Backbone (N,CA,C,O) : 12.12 +/- 3.59 A
## Backbone (N,CA,C,O) : 12.76 +/- 4.10 A
## Backbone (N,CA,C,O) : 12.41 +/- 3.78 A
Fitted:
## Backbone (N,CA,C,O) : 10.59 +/- 1.15 A
## Backbone (N,CA,C,O) : 9.05 +/- 1.36 A
## Backbone (N,CA,C,O) : 10.46 +/- 1.53 A
## Backbone (N,CA,C,O) : 9.82 +/- 1.17 A
## Backbone (N,CA,C,O) : 11.67 +/- 1.40 A
## Backbone (N,CA,C,O) : 12.09 +/- 2.53 A
## Backbone (N,CA,C,O) : 12.58 +/- 5.82 A
## Backbone (N,CA,C,O) : 10.77 +/- 3.45 A
## Backbone (N,CA,C,O) : 12.00 +/- 3.51 A
## Backbone (N,CA,C,O) : 11.17 +/- 2.82 A
- Re: [aria-discuss] ARIA Calculation Larger Protein, Kelly, Mark, 08/05/2020
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