On Mon, Jun 04, 2012, monica.imtech.res.in wrote:
>
> I made a complex of protein and a ligand by docking and after dock
> it came ok.I used it for MD for which i generated parameters for the
> ligand.I generated the frcmod and lib files successfully. Now the
> problem is that when i am saving the complex and converting in pdb and
> observing it, the ligand seems to be displaced from its position.Can
> anyone explain why is it so and wat shoul i do next????
You would need to tell us exactly what you did, not just "I am saving the
complex".
However, generally, after making the lib and frcmod files, you would load
those, along with one the the standard leaprc files (such as leaprc.ff12SB),
the use loadPdb to load the *original* pdb file that you obtained by docking,
which has both the protein and the ligand. In this way, the coordinates LEaP
is working with will be those from the docking study.
....dac
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Received on Mon Jun 04 2012 - 10:00:04 PDT
