AMBER Archive (2008)

Subject: Re: AMBER: bond command

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Jul 11 2008 - 07:00:48 CDT

Hi Ross

Thanks very much, this is very helpful!

Regards
Boutheina
On 10 Jul 2008, at 20:15, Ross Walker wrote:

> 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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