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.mail.shcnc.ac.cn
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Received on Thu Dec 24 2009 - 23:00:02 PST
