From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 11 2009 - 21:24:41 CDT
Hi Dalton,
dalton banks wrote:
> and I have some questions about these requirements.
>
> 1) Is there a standard procedure for creating such a box?
I recommend making a single copy of your molecule in molefacture, then
making a pdb file containing many copies of it arranged randomly or in a
lattice (requires a little bit of tcl scripting), and then run a (real)
equilibration.
> 2) I have psf files for my solvent molecules, but no top files; is
> there a way to create them from the psf files?
Not automatically, but you should be able to do so manually without too
much trouble if you understand the way topology files are laid out (see
the topology file tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/)
> 3) What is the key selection? This is something that's the same for
> all residues?
The key selection must occur for exactly one atom in each solvent
residue. Note that this allows the use of mixed solvents (for example,
if you have one solvent type containing atoms A, B, and C, and another
containing D, E, and F, then "name A D" would be a valid key selection).
> 4) This is the only documentatin I could find on Solvate, and it
> doesn't day much about how to use it from the command line (the
> tutorial doesn't help much more either). Is there more detailed
> documentation somewhere?
>
Most of the documentation is in the command line itself; try doing
package require solvate
solvate
and you will receive instructions. All of the command line options have
direct equivalents to the gui options (behind the scenes, the gui is
just building a solvate command line).
Best,
Peter
> Thanks,
> Dalton
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