[gmx-users] genbox give coord file more waters than top file

Berk Hess gmx3 at hotmail.com
Thu Mar 8 12:36:38 CET 2007

>From: "Mark Abraham" <mark.abraham at anu.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] genbox give coord file more waters than top file
>Date: Thu, 8 Mar 2007 22:27:01 +1100 (EST)
> > 8 mar 2007 kl. 01.32 skrev Mark Abraham:
> >
> >>> Dear gromacs guys
> >>>
> >>> Why would genbox put more water molecules in my .gro file than in
> >>> my .top
> >>> file? I'm sure all I have to do is edit the number in my top file,
> >>> but I
> >>> have not had this happen before, does anyone know of  a reason
> >>> that this
> >>> happens so I can fix my file?
> >>
> >> genbox doesn't read a top and produce that many solvent molecules.
> >> For a
> >> start, how does it know what shape you want them in? Read "man
> >> genbox",
> >> choose what you want to do, apply genbox, and then edit your .top
> >> so the
> >> number of waters agrees with what genbox produced... not the other way
> >> around.
> >>
> >> Mark
> >>
> >
> > I'm not so sure about that. genbox *does* take a top file as an
> > optional argument. genbox -h tells me:
> >
> > "Finally, genbox will optionally remove lines from your topology file
> > in which
> > a number of solvent molecules is already added, and adds a line with the
> > total number of solvent molecules in your coordinate file."
> >
> > I have never used this option, so I don't know exactly how it works,
> > but I expect it to do what William wants it to do.
>Maybe this works, I've never used it either... but the point is that the
>source of the information about how many waters to add comes from the
>genbox command line, not this .top file. I think William wanted the number
>of waters in his .top file to be added to his .gro file, and this is an
>ill-defined proposition.

This depends.
If the gro and top came out of pdb2gmx, pdb2gmx already recognized
the water molecules and wrote the gro and top files.
genbox is supposed to regonize these crystal waters in the gro and top file.
Normally it would just add a line for the added water molecules.
But genbox is so smart that it checks if the waters in the output 
match the number in the orginal top plus the added waters, and it corrects
the top if there is something wrong.
I would guess that this is where the error occurs.

Please file a bug report to bugzilla.gromacs.org with the gro and top file
and the command line used for genbox.


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