[gmx-users] Water molecule can not be settled

[Mark Abraham]

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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