AMBER Archive (2009)

Subject: [AMBER] MMGBSA

From: Zhongjie Liang (zjliang_at_mail.shcnc.ac.cn)
Date: Wed Dec 02 2009 - 19:17:44 CST


Dear experts,

     I am calculating the free energy (including entroy) of 100 structures,
but when it was doing the sanmin_com.26.out , where was error message as
follows:

 

   NSTEP ENERGY RMS GMAX NAME NUMBER

      1 NaN NaN 2.4098E+19 H10 4716

 

 BOND = 9543232.3761 ANGLE = NaN DIHED =
14825.2916

 VDWAALS = ************* EEL = 1012.6342 HBOND =
0.0000

 1-4 VDW = ************* 1-4 EEL = -1918.5531 RESTRAINT =
0.0000

 Frac coord min, max: -16959209342929.1 16959209342930.8

 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 wonder what exactly the restart file is , and how to restart the program.

Thanks for any suggestion!

                                            Zhongjie Liang

                                            zjliang_at_mail.shcnc.ac.cn

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