AMBER Archive (2004)

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

From: Kazuo Koyano (koyano_at_fsis.iis.u-tokyo.ac.jp)
Date: Mon Jun 21 2004 - 01:14:56 CDT

Dear Dr. T. Steinbrecher;

   Your perl script would be a great help to make the *.crg file, though
amber suite program now has been added in Amber 8. As Nan wrought, I noticed
that PBCAL=0 in ligand only. I input the charge of ligand in prep.file by
hand.
Sincerely Yours.
Kazuo Koyano

----- Original Message -----
From: "Thomas Steinbrecher" <steinbrt_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Saturday, June 12, 2004 4:53 AM
Subject: Re: AMBER: PBCAL in mm-pbsa calculation

> 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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