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

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 15 2019 - 08:14:09 CDT

Hello Philippe, one small note: when using the Euler angles, be aware that
not the entire space of rotations can be parameterized. Look up "gimbal
lock" for more details, but in essence when theta gets close to 180°, it
becomes impossible to define phi and psi separately.

This was the main reason why originally in Colvars, Euler angles were not
originally included (the same is also true in other packages like e.g.
Plumed). Only the multi-dimensional variable orientation (a quaternion)
was originally available. Unfortunately quaternions are also more
difficult to treat, especially if one requires computing a series of 1D
PMFs as done in the PLB protocol. The Euler angles were added later as
supplementary Tcl code, available in the SI of Haohao's paper.

The PLB protocol assumes that you will stay away from gimbal lock, and for
as long as you design the simulation so that the rotation is small, it
should work OK.

Lastly, for completeness take a look also at this paper:
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00447

Giacomo

On Thu, Aug 15, 2019 at 8:06 AM philippe Bourly <philippe.bourly20_at_gmail.com>
wrote:

> Thank you for your prompt reply !
>
> Regards,
>
> Philippe
>
>
> On Thu, Aug 15, 2019 at 1:22 PM Haohao Fu <fhh2626_at_gmail.com> wrote:
>
>> 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
>>>
>>>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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