Re: ABF with the RMSD colvar

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 15 2014 - 10:06:44 CDT

Yes, avoid using wrapAll in this case. Non covalently linked protein
fragments would be wrapped individually, and mess up the calculation of the
RMSD.

Giacomo

On Tue, Apr 15, 2014 at 6:22 AM, George Patargias <gpat_at_bioacademy.gr>wrote:

> Hello,
>
> I am trying to set up an ABF calculation using the RMSD colvar. The atom
> block of the colvar configuration file contains all the C-alpha atoms of a
> protein complex that consists of 7 (non covalently linked) subunits.
>
> I am trying to decide whether I need to exclude the wrapAll option (and
> use only wrapWater) on the basis of the recommendations found here
>
>
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132410000000000000
>
> I would really appreciate any tips on this
>
> Thanks!
>
>
> Dr. George Patargias
> Postdoctoral Research Fellow
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>
>
>
>
>
>
>
>
>

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