AMBER Archive (2008)

Subject: RE: AMBER: bond command

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 10 2008 - 14:15:53 CDT

Hi Boutheina,

In addition to what others have suggested I just wanted to point out that
you can always have leap read a text file containing a set of commands you
want it to read. Thus if you have some way that you could script the
generation of a text file containing all the bond commands, in exactly the
same format as you would type them in leap, one per line then you can just
source that file from within leap.

> source create_my_bonds.txt

And leap will sequentially process each line in that file - note you can use
this to make quite elaborate scripts, such as loading parameter files,
bonding, adding solvent, saving the prmtop and inpcrd files and quitting.
This way you can write code that does things like a 2D parameter scan and
have leap build you thousands of prmtop files without you having to do
anything interactively.

I hope this helps.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Boutheina Kerkeni
> Sent: Thursday, July 10, 2008 10:31 AM
> To: amber_at_scripps.edu
> Subject: AMBER: bond command
>
> Hi Amber users
>
>
> I have a question about bond command. I have to use it more than 100
> times, I wonder if there is a way to rather than typing each bond
> command into xleap,loading a whole file that contains these say 100
> bond lines in one go? If yes, how should such file be written, and
> what is the command to load it into xleap to build the model?
> Thanks for any light you could shed on this matter.
> Best Reagrds
> Boutheina
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