Re: restart mm_pbsa

From: Pascal Bonnet <>
Date: Thu 14 Nov 2002 15:13:06 +0000


This is one of the possibility.

Using the mm_pbsa script of AMBER6 (i didn't check for amber7), it is
easy using a script.
First extract your snapshots.
add "exit" after the line
$zcat $TRAJECTORY | $make_crd

Later, in three steps for example, run three mm_pbsa programs to
calculate the energies for snapshots 1 to 300, 301 to 600 and 601 to 900
If you look at the mm_pbsa code, you will find the line
Change this line with
number=1 in the first mm_pbsa run
number=301 in the second mm_pbsa run
number=601 in the third mm_pbsa run

Also, change the line
while [ -f "$name1""$number" ] ; do
while [ "$name1""$number" != "$name1"301 ] ; do for the first mm_pbsa
while [ "$name1""$number" != "$name1"601 ] ; do for the second mm_pbsa
while [ -f "$name1""$number" ] ; do for the last mm_pbsa run

Don't forget to comment the line (with #)
$zcat $TRAJECTORY | $make_crd if you don't want to process your
trajectory again into different snapshots for the three mm_pbsa runs.

Hope it helps

Layi Adekoya wrote:
> Hello Amber guys,
> I was wondering if it is possible to restart an mm_pbsa job.
> I have about 900 snapshots to be analysed and I think the job might get
> stuck somehow.
> Is it possible to restart the job? how? thanks in advance
> Regards,
> layi Adekoya
> --------------------------------------------------------
> For God so loved that He gave.........
> -----------------------------------------------------------

 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Oxford Road,
 Manchester, M13 9PL, U.K
 Tel:(+44) (0)161 275 2431
Received on Thu Nov 14 2002 - 07:13:06 PST
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