[gmx-users] Water molecule can not be settled

[Billy Williams-Noonan]

You could also try to reduce the time step of the minimisation, after first
attempting an* in vacuo* minimisation.

On 30 June 2016 at 01:32, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> First, minimise your protein in vacuo, so you have some confidence in your
> topology. Then solvate and minimise again. Your problem just looks like a
> standard case of not being gentle enough in an edge case.
>
> Mark
>
> On Wed, 29 Jun 2016 17:27 zeineb SI CHAIB <zeineb-14 at hotmail.com> wrote:
>
> > Dear gmx users,
> >
> > I'm having problems during my energy minimisation step, I tried different
> > options in the mdp file but I'm enable to fix the problem, I'm hoping
> that
> > you can help me with this.
> >
> > My system is a dimer that contain HEM, cofactor (Tetrahydrofolate, THF)
> > and arginin (substrate). I'm using CHARMM27 as a force field.
> >
> > At the beginning I fixed the problem of the HEM (perfectly linked with
> the
> > protein and completed its parameters).
> > In the second step, I generated the topology of THF with Swissparam's
> > server. I succeeded in running a molecular dynamic of 5ns. When I
> analysed
> > the dynamic the THF was in its right place and I didn't see any anormal
> > behaviour with my structure.
> >
> > Now, I'm trying to include the topology of the THF in CHARMM ff folder in
> > order to gain time and make things  more automatic. The modifications
> that
> > I did were:
> > - I added the residue to the .rtp file of CHARMM FF, only  [atoms] entry.
> > For the other entries [angles], [impropres]..etc, according to GROMACS
> > manual, they are optional so I did'nt add them.
> >
> > - I created an entry for THF in the .hdb file of CHARMM ff.
> >
> > After that, I run pdb2gmx and it succeeded to generate the topology. The
> > global structure looked OK but during energy minimisation, I got this
> Fatal
> > error:
> >
> > Fatal error:
> > step 36: Water molecule starting at atom 15431 can not be settled.
> > The atom 15431 belong to a water molecule and is far from the protein!!
> >
> >
> > Here are the parameters that I used in the mdp file:
> > integrator = steep
> > nsteps = 50000
> > nstxout = 1
> > ns_type = grid
> > energygrps  = Protein THG
> > emtol = 1000.0
> > emstep = 0.01
> >
> > ; Non bonded stuff (specific to CHARMM)
> > constraints = h-bonds
> > cutoff-scheme = Verlet
> > vdwtype = cutoff
> > vdw-modifier = force-switch
> > rlist = 1.2
> > rvdw = 1.2
> > rvdw-switch = 1.0
> > coulombtype = PME
> > rcoulomb = 1.2
> > DispCorr = no
> >
> > I tried to change the parameters (one changement each time) but it didn't
> > work:
> > 1- define = DFLEXIBLE
> > 2- define = DEPOSRE
> > 3- constraints = all-bonds
> > 4- emstep = 0,02
> >
> > I can't see where is the problem! Anyone can help me please.
> >
> > Regards.
> >
> > Zeineb
> >
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