[gmx-users] creating a solvent box

[Dallas Warren]

Is there something about the water molecule that is different to any
standard H2O?  If not, then simply use:

 

genbox_d -cs -box 4.0 6.0 4.0 -maxsol 3200

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Eric Shamay
Sent: Tuesday, 21 September 2010 10:17 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] creating a solvent box

 

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.

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? 

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