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 Sun Nov 04 2012 - 09:00:02 PST
