do this in 2 steps. first, align the protein using an rms command and mask
for the protein.
then do another rms command, for the ligand only, but put "nofit" at the end
of the line.
On Tue, Apr 27, 2010 at 8:42 PM, Yingjie Lin <linyj1984.gmail.com> wrote:
> Dear all,
>
> I've run 30ns simulation of a protein-ligand complex.
> The protein has 289 residues, and the 290th "residue" corresponds to the
> ligand.
>
> I am interested in checking how the ligand move in the simulation.
> To be more specific, I would like to calculate RMSD of the ligand with
> respect to the ligand in another file (named fileA.pdb).
>
> My script looks like this:
> =======
> trajin ../EQ/complex.1.trj.gz 1 1000 25
> trajin ../EQ/complex.2.trj.gz 1 1000 25
> ...
>
> center origin :1-290
> image origin center
>
> rms first mass out complex_rmsf_ca.dat .CA
>
> strip :291-119999999
>
> reference fileA.pdb :1-290
> rms reference mass out ligand_rmsf.dat :290
> ======
> I am not sure about the last two lines. Since I want to "align the protein
> and then calculate RMSD for the ligand",
> which of the following should I use?
> 'reference fileA.pdb :1-290'
> or 'reference fileA.pdb :1-289'
> or 'reference fileA.pdb :290'
>
>
> Thanks a lot!
>
> Yingjie
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 27 2010 - 18:30:03 PDT
