: [AMBER] MMGBSA error

From: Zhongjie Liang <zjliang.mail.shcnc.ac.cn>
Date: Wed, 23 Dec 2009 21:12:07 +0800

Thanks for your attention! 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 dont understand the principle of the MM/GBSA quite well, but it seems
that it used the virtual box in the calculation.

   Thanks for your help.

 

                       Zhongjie Liang

                       zjliang.mail.shcnc.ac.cn

 

-----ʼԭ-----
: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org]
Carlos Simmerling
ʱ: 20091222 21:06
ռ: AMBER Mailing List
: Re: [AMBER] MMGBSA error

 

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.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.

>

>

>

>

>

>

>

>

>

>

>

>

>

> Zhongjie Liang

>

> zjliang.mail.shcnc.ac.cn

>

> _______________________________________________

> AMBER mailing list

> AMBER.ambermd.org

> http://lists.ambermd.org/mailman/listinfo/amber

>

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Received on Wed Dec 23 2009 - 05:30:04 PST
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