AMBER Archive (2002)

Subject: Re: restart mm_pbsa

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Thu Nov 14 2002 - 09:13:06 CST

Hi,

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
respectively.
If you look at the mm_pbsa code, you will find the line
number=1
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
to
while [ "$name1""$number" != "$name1"301 ] ; do for the first mm_pbsa
run
while [ "$name1""$number" != "$name1"601 ] ; do for the second mm_pbsa
run
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
pascal

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
 http://www.man.ac.uk/~mbpsspb3