Hi,
On Fri, Jun 28, 2013 at 1:43 PM, Hunter Brown <bassoongoon.earthlink.net> wrote:
> Okay. Thanks. The reason I used VMD to ionize it was because I wanted specific box dimensions (a little bit of padding in two dimensions, and a bit of negative padding in the other dimension). My mentor wanted me to make it so that part of the protein is sticking out of the waterbox, for some reason having to do with periodic boundary conditions. The B1 tutorial never explained how to adjust dimensions of the solvation box like that. Also, I used VMD because the ionization is really easy, neutralizing and setting the molarity (0.1M NaCl).
>
> Can I use LEaP to create the box dimensions I like, or is it all done automatically as it was in the B1 tutorial. Also, can I use leap to neutralize and then set to 0.10M?
You can specify buffer values for individual dimensions by providing a
List as the 'buffer' argument of the "solvateBox" command (e.g.
solvatebox mol TIP3PBOX {<bufx> <bufy> <bufz>}), although this won't
allow exact specification of the box size. After you've solvated your
system in LEaP and written out a topology/restart you could
potentially set explicit box dimensions by modifying the last line of
the restart file, which is 6 numbers representing box {X Y Z Alpha
Beta Gamma}. However, unless your initial system is very
well-equilibrated the box dimensions can and should change as the
density equilibrates. Note also that under periodic boundary
conditions there is no 'sticking out' of the box; your system is
infinitely repeated in all dimensions, so the part that appears to be
'sticking out' is really just interacting with the next cell (you can
verify this visually because there will appear to be a 'gap' in the
solvent in the opposite dimension).
You can add ions with LEaP (see addIons, addIonsRand) but you can't
set an explicit concentration. You could calculate an approximate
concentration based on your box dimensions and add that many ions if
necessary. If you really need to use VMD to build your system you
could potentially create name maps in leap using the "addPdbAtomMap"
and "addPdbResMap" commands to try and translate names to what LEaP
expects. Also, even though you can't set box dimensions explicitly in
LEaP, if you don't use 'solvateBox' or 'solvateOct' you still need to
use at least the 'setBox' command so that your topology will have the
proper box-related flags set (note 'setBox' is for orthogonal boxes
only). Another program like Packmol may be able to do what you want
but I have no experience using it. Others on the list may have better
ideas.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jun 28 2013 - 13:30:02 PDT
