AMBER Archive (2009)

Subject: [AMBER] MMGBSA error

From: Zhongjie Liang (zjliang_at_mail.shcnc.ac.cn)
Date: Fri Dec 25 2009 - 00:59:16 CST

Dear users£¬

  I got 100 snapshots from the trajectory file. My input parameter file was
as follows:

 

@GENERAL

PREFIX snaps

PATH ./

COMPLEX 1

RECEPTOR 1

LIGAND 1

COMPT ./complex.top

RECPT ./protein.top

LIGPT ./lig.top

GC 0

AS 0

DC 0

MM 1

GB 1

PB 0

MS 0

NM 1

@MM

DIELC 1.0

@GB

IGB 2

GBSA 1

SALTCON 0.00

EXTDIEL 80.0

INTDIEL 1.0

SURFTEN 0.0072

SURFOFF 0.00

@NM

DIELC 4

MAXCYC 10000

DRMS 0.01

 

And the sanmin_com.in file generated by mmpbsa.pl was as follows:

 

&cntrl

  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

&end

 &ewald

  eedmeth= 5,

 &end

 

I know it would calculate the free energy of each structure one by one. When
it was doing the minimization of complex 26, it stopped and the error
message in the sanmin_com.26.out was as follow:

 

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
that it used the virtual box in the calculation.

How to deal with the problem except removing the 26 structures. Any
suggestion would be appreciated.

 

                                   Zhongjie Liang

                                    zjliang_at_mail.shcnc.ac.cn

 

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