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.mail.shcnc.ac.cn
-----ÓʼþÔ¼þ-----
·¢¼þÈË: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] ´ú±í
Carlos Simmerling
·¢ËÍʱ¼ä: 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.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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 23 2009 - 05:30:04 PST
