On Mon, 22 Apr 2019 at 08:13, Prasanth G, Research Scholar <
prasanthghanta.sssihl.edu.in> wrote:
> Dear Ray Luo,
>
> Thank you for your response. Could you please let me know, how to carry out
> the "rmsd of the realative affinities for the ligands".
> Is this the same as carrying out RMSD of the ligand through the trajectory?
>
I think that he means to calculate the Root Mean Squared Error (RMSE) of
the energies, which you can do by writing a few lines of Python or R code.
Do not confuse it with the coordinate RMSD, which is another thing.
> ----
> $ cpptraj
> >parm comdry.prmtop
> >trajin production_no_wat_ions_0_30.nc (complex of protein and ligand
> without water and ions)
> >rmsd ToFirst :671.C,N,O out ligand_0_30.rmsd time 0.002
> >go
> ----
> Calculation of delta delta G (as i understand) could be done with the
> values obtained from the final results obtained (from PB and GB
> caluculations).
> example: delta delta G = delta G1- delta G2 (separately for GB and PB)
>
> Please correct me if I am wrong.
> Also, do you feel that increasing the salt concentration has any effect in
> reducing the difference.
> -------
> In response to Prof Luo's response..
> Prasanth,
>
> I suggest that you look at the overall correlation and rmsd of
> relative affinities (delta delta G's) for all ligands instead of the
> agreement of the delta G of a single ligand.
>
> All the best,
> Ray
> --
> Regards,
> Prasanth.
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>
--
======================================================================
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
&
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic
email: tevang3.gmail.com, Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
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Received on Mon Apr 22 2019 - 07:00:02 PDT
