[gmx-users] creating a solvent box

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 21 02:23:46 CEST 2010

Eric Shamay wrote:
> 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 
> database
> 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.

Since you've already got sw.itp, then there's no point at all in running 
pdb2gmx, whose sole purpose is to create topologies.  Since you've got that, 
your life should be easy:

#include (force field)

#include "sw.itp"

[ system ]

[ molecules ]
SW  3200

> 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 box?

Above you state that sw_box.pdb contains the system you want.  If that's the 
case, there's no need for genbox at all.  Use sw_box.pdb as your coordinate file 
input into grompp in conjunction to the skeleton topology I have shown above.

If your goal is simply to obtain a .gro file, just use editconf.  But do note 
that there is no requirement whatsoever that you have to use .gro format.  Most 
Gromacs tools are extremely flexible, and a .pdb file will work just fine.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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