Hello All,
I have a kinase and a acetonitrile bound to the surface of the protein.
I am trying to analyse the movement of the ligand from the pocket during my TI runs, for each lambda window.
Here is a sample input file I am using for lambda=0.00922
parm C3N_solvated.prmtop
trajin C3N_solvated_prod.mdcrd 1 last 1
center mass origin :1-273
image origin center
reference ../complex_WAT_box_SITE1.pdb
strip :WAT
strip :Na+
rms reference mass out backbone_0.00922_aligned_RMSD.txt :2-272.CA,C,N
rms C3N_site1 :C3N&!.H= nofit mass out lig_prob_0.00922_rmsd.dat
go
Residue 1 and 273 are my ACE and NME caps respectively...Residue 2 to 272 is my protein atoms.
I am not sure if I should use “nofit” in my rms command line?
Any insights would be super helpful.
Thanks
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Received on Sat Oct 03 2020 - 08:30:02 PDT
