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
ligand with its correct charge to the *.crg file.
This perl script might help:
-------------------------
#!/usr/bin/perl -w
while (<>) {
/.{7}(...).*\s+([- ]\d\.\d{4})\d*/;
if ($1) {print "$1 LIG $2\n";}
}
-------------------------
(There are three spaces after $1, six after LIG, if email-format
should scramble it)
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-
and n- terminal residues, you cannot just use the file provided with
mm_pbsa, which was made for another biochemical system.
You could also use pbsa from amber8, it doesn't need a crg-file.
Regards,
Thomas
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Received on Fri Jun 11 2004 - 21:53:00 PDT
