AMBER Archive (2004)

Subject: Re: AMBER: PBCAL in mm-pbsa calculation

From: Thomas Steinbrecher (
Date: Fri Jun 11 2004 - 14:53:21 CDT

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.



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