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AMBER Archive (2004)Subject: Re: AMBER: PBCAL in mm-pbsa calculation
From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Hi Nan,
my_amber*.crd is the right file but you have to edit it.
First look into your ligand prep file and add a line for each atom in the
This perl script might help:
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while (<>) {
(There are three spaces after $1, six after LIG, if email-format
just change LIG to the pdb-name of your ligand and run
script <prep-file>
it should give you the necessary *.crd file entries.
Also check the *.crg file if the correct protein-aminoacids are set as c-
You could also use pbsa from amber8, it doesn't need a crg-file.
Regards,
Thomas
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