Re: [AMBER] Sander bomb: how to create a larger box

From: Ruth Helena Tichauer <>
Date: Mon, 1 Aug 2016 12:53:51 +0200

Dear Bilal,

Thank you for your answer!

Indeed, that’s what I had first thought.. but I was hoping for a solution anyway, and I figured out a scheme such that:
As the numbering of the water molecules assigned by tleap would be the same, I would replace the new coordinates of the water molecules by the ones on the restart file and, as there would be more water molecules than previously, I would keep the coordinates assigned by tleap for these extra water molecules (and hopefully there would be a way to also get velocities for these extra water molecules).

I thought that such a procedure would be achievable with parmed and so I was hoping some guiding to do so.. Does anyone know if this would be possible?

Thanks in advance for any suggestion,


> On 30 Jul 2016, at 22:58, Bilal Nizami <> wrote:
> Dear Ruth,
> According to my understand, this is not possible. If you remove the water
> molecule from your trajectory and introduce new ones, new water molecules
> would have different coordinates than those in your restart file. I guess,
> program won't be able to resolve this.
> Regards,
> 2016-07-28 16:48 GMT+02:00 Ruth Helena Tichauer <>:
>> Dear amber users,
>> I am running a QM/MM molecular dynamics simulation and I get the following
>> error message:
>> SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
>> QM region + cutoff larger than box
>> cannot continue, need larger box.
>> I understand why this is happening and to solve this behaviour I wish to
>> create a larger water box around my protein rather than decrease the value
>> of the cutoff.
>> I was thinking to strip all the water molecules and then create a new box
>> and new parameters with tleap but then, if I understand correct, I would
>> have to start all over (starting from 0 ps). So, is there any way such
>> that, I would be able to have a bigger water box and use the restart file
>> from the previous run in order to continue my simulation from where it has
>> been stopped?
>> Thank you for any help,
>> Ruth
>> _______________________________________________
>> AMBER mailing list
> --
> *Bilal Nizami*
> School of Health Sciences
> University of KwaZulu-Natal
> Durban
> 4000
> South Africa
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> Email:
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Received on Mon Aug 01 2016 - 04:00:02 PDT
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