Thanks Jason that's great stuff.
The tutorials on the amber page seem to be a little outdated, do you know where / if there are new / maintained beginner / intermediate amber tutorials?
Thanks!!
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
On Nov 4, 2012, at 6:40 PM, Jason Swails wrote:
> On Sun, Nov 4, 2012 at 10:24 AM, Fabian Glaser <fglaser.technion.ac.il>wrote:
>
>> Thanks!
>>
>> That's working now, but of course the next stage is not:
>>
>>> solvateBox mol WATBOX216 10
>> solvateBox: Argument #2 is type String must be of type: [unit]
>> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>>
>> Would you be so kind to tell me what is wrong now?
>>> solvateBox mol WATBOX216 10
>> Is copied from the tutorial.....
>>
>
> Hmm, I'm not sure why the tutorial asks for WATBOX216, that unit does not
> exist in the force fields that I use. One nice thing about tleap is that
> it has pretty good introspective commands. This means that you can ask
> tleap itself what "things" it knows about, what commands are available, and
> how to use them.
>
> For example, just running "help" gives you a list of all commands that you
> can run. If you say "help <command>", it will tell you how to use that
> command. The "list" command will list all of the UNITs that tleap knows
> about. The "desc" command will dump a full description that tleap is
> carrying around about a particular unit or part of a unit. I recommend
> that you play around with some of these commands in tleap to try and get a
> better working knowledge of how the program works (it's a time investment
> that will pay itself back in the future, in my opinion).
>
> What the error message you got is telling you is that Argument #2
> (<solvent>) must be of type [unit], which means that it MUST appear when
> you run the "list" command (because it lists all known UNITs). You will
> see that this is clearly not the case, suggesting that the person that
> created the tutorial was using their own custom leaprc file that somehow
> defined WATBOX216 (or maybe it's a much older force field?). So what you
> need to do is to replace WATBOX216 with another UNIT that exists (that is,
> it is printed out by "list") that is a pre-equilibrated TIP3P water box
> (look for TIP3PBOX).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Nov 05 2012 - 06:30:04 PST
