[gmx-users] putting extra molecules in the box with genbox

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 6 16:00:10 CET 2009

Oliver Masur wrote:


> So i built up my box, then put h2po4 in (and then a counterione) by using
> "genbox -cp protein.gro -cs spc216.gro -ci h2po4.gro -nmol 1 -shell 1 
> -seed int -o out.gro -p protein.top"
> this part works, except that genbox doesn't update protein.top for 
> anything else than the water solvens, and i had to put in the h2po4 
> group myself.

Works, as in, it correctly places your H2PO4 in the box, or just that the 
command runs without error?  I don't know about the problem with updating the 
topology, but you've got a lot going on at once; maybe that combination breaks 
something.  You could do everything in two steps to make life easier:

genbox -cp protein.gro -ci h2po4.gro -nmol 1 -p protein.top
genbox -cp out.gro -cs spc216.gro -p protein.top

> When i try to grompp then this error occures:
> "no such moleculetype h2po4"

That comes up because you either haven't included the right .itp for H2PO4, or 
you've included it in the wrong order.

> And before that, i probably mixed up some atom names because i.e. "no 
> such atomtype HO" occured.
> The whole thing works for normal ions like Na+ or Cl- where i just had 
> to write the gro file!

Which .gro file did you have to write?  Inserting Na+ or Cl- is the purpose of 
genion; were you doing this manually?


> If someone sees my mistake, or maybe can tell me how extra molecules 
> really can be put in the box, i'd immensely appreciate it.
> thank you up-front,
> Oliver
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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