Re: [AMBER] Sander QMMM Bomb Problem

From: Gustavo Seabra <>
Date: Tue, 19 May 2015 14:13:42 -0300

Hi Alican,

Are you sure it is your ligand that is drifting? You mention that you have “two water molecules and a small ligand” in the water box. Do you mean the two water molecules are treated as QM? In this case, is there any chance that it can be the waters that are drifting?

Gustavo Seabra

> Em 14/05/2015, à(s) 16:56, Gulsevin,Alican <> escreveu:
> I posted this a while ago, but since no one replied since then, I am
> reposting.
> Hello,
> I am trying to do umbrella sampling on a system of two water molecules
> and a small ligand of ~20 atoms in an octahedral water box. I use
> scc-dftb for the qm part and the only mm atoms are TIP3P waters.
> However, my calculations crash after some time, giving the good old
> "sander qmmm bomb error". Now, I am aware this is happening because my
> molecule drifts away to the edges of the water box to a distance less
> than the qm cutoff defined. Since my system is so small, drifting in
> the
> solvent is inevitable. I tried increasing the solvent box up to 24A and
> increasing the box size postpones the bitter end, but having to add so
> many water molecules for a QM system of 25 atoms is crippling. My
> question is, is there a way I can recenter the water box around the
> ligand after a certain number of steps. Or else, what could you suggest
> to overcome this problem?
> Thanks,
> Alican
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Received on Tue May 19 2015 - 10:30:03 PDT
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