Hi,
You've got 2 rms commands, the first one fits on residues 2 to 272 of
your protein, the next is the no-fit rmsd of your ligand (i.e. the
RMSD of the ligand in the reference frame of the protein), which seems
like what you want. Does this answer your question?
-Dan
On Sat, Oct 3, 2020 at 11:08 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 04 2020 - 07:00:03 PDT
