AMBER Archive (2009)
Subject: ´ð¸´: [AMBER] MMGBSA error

From: Zhongjie Liang (zjliang_at_mail.shcnc.ac.cn)
Date: Wed Dec 23 2009 - 07:12:07 CST

Previous message: FyD: "Re: [AMBER] atom type"
In reply to: Carlos Simmerling: "Re: [AMBER] MMGBSA error"
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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 don¡¯t 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_at_mail.shcnc.ac.cn

-----ÓÊ¼þÔ¼þ-----
·¢¼þÈË: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] ´ú±í
Carlos Simmerling
·¢ËÍÊ±¼ä: 2009Äê12ÔÂ22ÈÕ 21:06
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: 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_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.