Ligand Bound.

From: kparra_at_mail.usf.edu
Date: Wed Nov 14 2007 - 12:30:27 CST

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Hi!
I am a new user of NAMD. Could you please tell me if NAMD can simulate the
process of breakingb a small ligand bound on a protein, and its
conformational changes during this process?

I already made a run of the protein bounded to the small ligand, what I
want is to continue this run with the ligand present but without the bound
between this protein and this ligand. I have a pdb file from the last
state of the protein in the last run (with the water box).

Could I make a new psf file which contains protein, water, and ligand
unbounded to continue the run? I tried but I got psfgen errors when I
include the protein, water, and the unbounded ligand. Psfgen could not
coordinate water molecules.

Thanks so much for your possible help.

Any information will be appreciated!

Katherine.

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