Re: [AMBER] MM PBSA - clarification

From: Prasanth G, Research Scholar <>
Date: Mon, 22 Apr 2019 11:47:41 +0530

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?
$ cpptraj
>parm comdry.prmtop
>trajin (complex of protein and ligand
without water and ions)
>rmsd ToFirst :671.C,N,O out ligand_0_30.rmsd time 0.002
Calculation of delta delta G (as i understand) could be done with the
values obtained from the final results obtained (from PB and GB
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..
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,
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Received on Sun Apr 21 2019 - 23:30:02 PDT
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