[gmx-users] creating a solvent box

[Justin A. Lemkul]

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 ]
SW

[ 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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