[gmx-users] creating a solvent box

Eric Shamay eshamay at uoregon.edu
Tue Sep 21 02:17:21 CEST 2010

This may very well be a simple problem, but I have found little in the way
of documentation that helped me get it to work:

I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd
like to use the water model specified in sw.itp (polarizable & flexible). In
the working directory I have a pdb file that specifies exactly the final
system that I want to use, but I cannot generate a .gro file from this pdb
file in order to run a simulation. I've tried 2 routes to accomplish this:

1) pdb2gmx - I've attempted to use this program as follows:
'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp'

This reports a fatal error: Residue 'SW' not found in residue topology

Because the sw.itp file defines SW as the molecule name, and again as the
residue name, I assumed that's what I'd want to appear in my pdb file as
well. I've tried every combination of force fields and water model to see if
that would do anything, but to no avail.

2) genbox - I tried to generate a solvent box using the pdb file as the
solvent definition:

'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200'

This made it look as though it was running, but after a very long time it
did not return and produce a .gro file I could use. It's as if the program
just hung or got stuck in some overly complicated solvation routine.

I realize that the SW residue is not defined in the standard force fields,
and so that's why I want to include sw.itp. Is there a way to generate this
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