[gmx-users] Incorrectly added water molecule by genbox.

[Dawid das]

Thank you Mark but it seems that removing one water molecule does not do
any good. I removed another one and the error arises again for another one.
What else can I do if water does not settle during minimization?
That's my minimize.mdp file.

title                    = minimization of mCherry
; this is a comment
integrator               = cg ; (other: steep, l-bfgs)
emtol                    = 1000
emstep                   = 0.01
nsteps                   = 2000
nstlist                  = 1
ns_type                  = grid
nstenergy                = 50
rlist                    = 1.0
coulombtype              = PME
rcoulomb                 = 1.0
rvdw                     = 1.0
pbc                      = xyz
freezegrps               = Protein
freezedim                = Y Y Y



2014-07-03 9:55 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> On Thu, Jul 3, 2014 at 9:17 AM, Dawid das <addiw7 at googlemail.com> wrote:
>
> > Hi,
> >
> > I have a following issue. Genbox seems to add a water molecule inside
> small
> > protein cavity and it does not belong there. Can I manually remove it
> from
> > *gro file?
>
>
> Yes, but you need to make a matching change to the [molecules] section of
> any matching .top file.
>
>
> > What with the numbering of residues in this situation?
>
>
> Immaterial. The only important thing in such cases is that there is a
> change; the values or the delta-value is not noticed.
>
> Mark
>
>
> > The
> > problem is that this water molecule can't be settled during minimization
> > and it spoils everything.
> >
> > Dawid
> > --
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