Amber users and developers,
I'm new to the approach of thermodynamic integration though I'm familiar with the theory. Here I have attached my inputs for a two-step ligand disappearing simulation. I would really appreciate it if you could give your thoughts and suggestions in this regard.
In my prmtop, I included duplicates of my ligand. I used the crgmask=' ' in Amber to perturb charges to 0. So, residue 'UNL' is my end state for the first step.
The initial parameter file (ligands_ti.parm7) was created without neutralizing the charges in tleap.
Coordinates for sampling (eq4.rst7) were obtained after 650 ps equilibration (4x100 ps + 250 ps).
In the first step, TMP ligand goes to no charges state UNL. Then I'm using the softcore potential approach to remove vdW interactions in second step. Here, my crgmask=' ' includes both residues because I'm starting from a charge 0 state. Please let me know your thoughts on this.
Thanks in advance,
Senal Dinuka
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Received on Tue Oct 27 2020 - 10:30:03 PDT
