HI ALL!!
I have generated a one molar system with 4 solute
molecules. I have to carry out and umbrella sampling for this system wherein
a proton is transferred from phenol to the imine. Out of all the
phenol-imine residues present in the system,I am considering residues 22 and
23 for the proton transfer. My problem is the calculations stop with error:
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 4.0000
Coord Lower Upper Size Radius of largest sphere inside unit
cell
X -9.745 9.611 19.357 11.528
Y -5.919 11.077 16.996 11.528
Z -12.188 11.060 23.248 11.528
****************************************************
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box.
Now the rst file show Box dimension: 28.9740000 23.0560000 27.7450000
90.0000000 90.0000000 90.0000000
When I try to run calculation with cut and qmcut value of 8.0, the
calculation even doesn't initiate. So to check if QM is applied to proper
residues, I reduced the cut value to 4 (I referred to the mailing list
letters for this). here the calculation begin which eventually ends after
some 13000 steps.
I tried to increase the box size by adding some methanol moelcules ( a box
size around 70 70 70), still the same error appears.
If the QM is applied to only oneresidue, the calculation runs smoothly, but
not for two residues.
How to work QMMM with QM on 2 residues?
Please find attached all the needed files which were generated and point out
mistake or suggestions to work out this problem
Kaustubh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 06 2011 - 08:00:04 PDT
