AMBER Archive (2009)

Subject: Re: [AMBER] MMGBSA error

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 22 2009 - 07:05:41 CST

please post more details about what you are doing. there should be no
virtual box in a GBSA calculation.

On Tue, Dec 22, 2009 at 8:04 AM, Zhongjie Liang <zjliang_at_mail.shcnc.ac.cn>wrote:

> Dear users,
>
> I was doing the MM/GBSA to calculate the free energy . The error
> message is as follows:
>
> The system has extended beyond
>
> the extent of the virtual box.
>
> Restarting sander will recalculate
>
> a new virtual box with 30 Angstroms
>
> extra on each side, if there is a
>
> restart file for this configuration.
>
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
>
> Atom out of bounds. If a restart has been written,
>
> restarting should resolve the error
>
>
>
> It seems that the system is out of the box the sander created. I wonder how
> to restart the calculation.
>
> Any suggestion would be appreciated.
>
>
>
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>
>
> Zhongjie Liang
>
> zjliang_at_mail.shcnc.ac.cn
>
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