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

From: Bilal Nizami <>
Date: Sat, 30 Jul 2016 22:58:29 +0200

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.


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
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*Bilal Nizami*
School of Health Sciences
University of KwaZulu-Natal
South Africa
AMBER mailing list
Received on Sat Jul 30 2016 - 14:00:02 PDT
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