For the record, it is possible to choose your box size.
I remember I tried doing this a few times.
I remember the first couple times I was not very careful and sander
would die by segmentation fault.
Although this may not fix all of your problems, but you might want to
take a look at tutorial 13
http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html
In this tutorial, the author manually specifies the periodic box dimensions.
(Of course, you must make sure that the box you want to use is
compatible with the solvent you have added. For this reason, I would
not use leap, xleap or tleap to solvate your system. I would use some
other program to construct a PDB file which includes the solvent
already. VMD has a useful extension for doing this in version 1.8.7.
"Extensions"->"Modeling"->"Add Solvent box". Tutorial #13 has another
program for doing this. I'm sure there are many others programs.)
--- synopsis of tutorial #13: ---
Once you have a PDB file containing a solvated structure,
load it into leap and use the "setBox" command to create a box.
example:
solvatedmol = loadpdb "solvatedmol.pdb"
setBox solvatedmol vdw {31.0 31.0 31.0}
saveAmberParm solvatedmol solvatedmol.top solvatedmol.crd
(You can use "centers" instead of "vdw". It doesn't matter. The
numbers (31.0) don't matter either. We will have to fix the box size
later. The tutorial uses "setBox solvatedmol vdw 1.0")
You can then edit the first 3 numbers on the last line of the CRD
file, to select the box size you want. (Or use the "ChBox" program
included in tutorial 13 to do this for you.) That's all you need to
do. ...I think...
-- Do we need to edit the TOP file? --
I don't think we need to make any changes to the TOP file.
(There is a section of this file named "%FLAG BOX_DIMENSIONS" in the
top file with some numbers below it. These numbers will be wrong. If
you're truly paranoid, you can edit the last 3 numbers on the line at
this location in the file to match your box size. However I am under
the impression that this is not necessary. Somebody please correct me
if I'm wrong.)
-- visualization --
You can check to see that the periodic boundary conditions in the CRD
file is correct using VMD. (First make a copy of the CRD file you
created in leap, and delete the first line from this file. Load the
TOP file in VMD. Then load the edited CRD file in VMD, and select the
format: "Amber Coordinates with Periodic Box".) Using the menu
"Graphics"->"Representations", click on the "Periodic" tab, and click
on the +X,-X, +Y,-Y,+Z,-Z boxes. It is helpful to use the menu option
"Display"->"Orthographic".)
Good luck
Andrew
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Received on Wed Sep 29 2010 - 17:30:03 PDT
