On Thu, Jan 14, 2016 at 7:41 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Dear all,
>
> I just installed AmberTools15 and completed the first tutorials. I am
> proceeding on the tutorial A08, but I am issuing problems with tleap.
>
> First of all, I don't have a leaprc file, and I would like to have
> suggestions from you on how to create one that would be ok for a
> costant pH MD run on a protein containing a chromofore.
>
There's a constant pH leaprc file already -- leaprc.constph. All it does
is load the force field for which the constant pH reference energies were
derived, sets the appropriate solvation radii for which the reference
energies were derived, and loads the extra residue templates needed for
carboxylate side-chains (AS4 and GL4). So while it's not *needed*, I'd
highly recommend using it.
That said, titrating a residue that is not one of the standard 5 or 6
supported residues (ASP, GLU, HIS, LYS, TYR, and CYS) is a challenging
problem (so if the chromophore itself titrates, this will be much harder
than if standard residues around it titrate).
>
> Then, I get an error from solvateBox:
>
> > solvateBox mol WATBOX216 10
>
Where did you get "WATBOX216"? That is not a legitimate unit in any of
the standard force fields. Try TIP3PBOX instead. You can use the command
"list" to get a list of all recognized units in tleap.
> solvateBox: Argument #2 is type String must be of type: [unit]
>
This is telling you that, indeed, WATBOX216 means nothing to leap here.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 14 2016 - 20:30:04 PST
