Hi,
I want to use US-QM/MM simulations to determine the activation barrier of
an enzyme catalyzing a transformation of its substrate. I have heated and
equilibrated the system classically and now I want to do a QM/MM
minimization and equilibration before a production run with umbrella
sampling. I am using AMBER12 and Gaussian09.
My minimization input file looks like this:
minimization system
&cntrl
imin = 1,
maxcyc=2000, ncyc = 500,
ntpr = 10, ntwr = 1000,
ntf = 1, ntc = 1, cut = 8.0,
ntb = 1, ntp = 0,
ifqnt = 1,
nmropt = 1, ioutfm = 1,
&end
&wt
type='END',
&end
DISANG=disang
&qmmm
qmmask =
'.1-35,2139-2140,2152-2165,3408-3409,3419-3435,5509-5514,7431-7441'
qmcharge = -1,
qm_theory = 'EXTERN',
qm_ewald = 0,
qmmm_switch = 1, r_switch_hi = 8.0, r_switch_lo = 6.0,
qmmm_int = 2,
qmshake = 0,
printdipole = 1,
writepdb = 1,
qmcut = 500.0,
scfconv = 1.0d-9,
diag_routine = 0,
peptide_corr = 1,
/
&gau
num_threads=8,
charge = -1,
/
The disang file is as follows:
Harmonic distance restraints
&rst
iat=18,3428,
r1=-0.0, r2=1.7, r3=1.7, r4=90.0,
rk2=200.0, rk3=200.0,
/
And the gau_job.tpl:
#P wB97XD/6-31+G(d,p) OPT nosymm
qmmm
-1 1
When I run this, it aborts with the following message (I have also attached
the full output file):
****************************************************
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 500.0000
Coord Lower Upper Size Radius of largest sphere inside unit
cell
X -504.740 503.106 1007.846 34.633
Y -507.088 508.633 1015.721 34.633
Z -508.134 510.109 1018.243 34.633
****************************************************
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box.
Setting qmcut to around 100A has the same effect. If I set qmcut to a lower
value, e.g. 15 A, it crashes with the following message:
SANDER BOMB in subroutine get_gau_forces (qm2_extern_gau_module)
Error with system call (executing Gaussian)
Will quit now.
Which I assume is due to the cutoff not being large enough (?)
It also caught my attention that the gau_job.inp file produced in this run
looks like:
%chk=gau_job.chk
%NProcShared=8
#P BLYP/6-31G* SCF=(Conver=8) Force Punch=Derivatives NoSymm Charge
Prop=(Field,Read)
Gaussian run using SANDER external interface.
-1 1
which means that it did not read the functional and basis set I gave it,
although it did read the number of processors to use from the AMBER input
file.
So, to sum up, my questions are:
1) What should I do in order to get a cutoff large enough but that at the
same time does not cause this sander bomb?
2) Why is Gaussian not reading the .tpl file?
Thank you in advance for your help.
Tamara
--
*P *Please consider the environment before printing my email.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 17 2013 - 18:00:03 PDT
