AMBER Archive (2009)
Subject: 答复: [AMBER] MMGBSA error
From: Zhongjie Liang (zjliang_at_mail.shcnc.ac.cn)
Thanks for your attention! I got 100 snapshots from the trajectory file. My
And the sanmin_com.in file generated by mmpbsa.pl was as follows:
ntxo = 0,
ntf = 1, ntb = 0,
dielc = 4,
cut = 99.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 10000,
ncyc = 0, drms = 0.01
I know it would calculate the free energy of each structure one by one. When
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
I don’t understand the principle of the MM/GBSA quite well, but it seems
Thanks for your help.
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
> 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
> to restart the calculation.
> Any suggestion would be appreciated.
> Zhongjie Liang
> AMBER mailing list
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