Re: Standard binding free energy protein-ligand (ABF)

From: Haohao Fu (fhh2626_at_gmail.com)
Date: Thu Aug 15 2019 - 06:22:07 CDT

Hi, Philippe,

Yes, they are in principle the same. The new Euler angles can be found in
the SI of https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791
Using the new definition of polar and Euler angles, no explicit selection
of atom groups is needed.

If you want to calculate the standard binding free energies by the
Geometric route, you can use the BFEE plugin (
https://pubs.acs.org/doi/abs/10.1021%2Facs.jcim.7b00695) to automate the
process.

Best,
Haohao

philippe Bourly <philippe.bourly20_at_gmail.com> 于2019年8月15日周四 下午7:12写道:

> Hello,
>
> I am sorry for the last email, apparently you received only one part of my
> message.
>
> I would like to calculate the standard binding free energy between a
> peptide and a protein using the same method as the NAMD protein-ligand
> tutorial.
>
> I saw that the colvars 'polarTheta' and 'PolarPhi' are available on
> NAMD2.13. Is it the same polar angles described in the tutorial (they used
> the "dihedral" keywords on the tutorial)? What about the Euler angles
> (Theta,Phi and Psi)? Are they available too on this new version of NAMD?
>
> Thank you,
>
> Philippe
>
>

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