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

From: philippe Bourly (philippe.bourly20_at_gmail.com)
Date: Thu Aug 15 2019 - 07:04:44 CDT

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
>>
>>

This archive was generated by hypermail 2.1.6 : Fri Dec 06 2019 - 23:20:46 CST