[AMBER] Gaussian through sander-cutoffs

From: Aseel Bala <balaahme.msu.edu>
Date: Mon, 24 Oct 2016 15:11:44 -0400

Hi everyone,


I am trying to run Gaussian through sander to do QM/MM simulations. For one frame, I center a particular molecule, define a cutoff and run sander. Then I choose a different molecule in the same frame, center that one and rerun the calculation. My input file is as follows:

Testing tutorial on website for QMMM with Gaussian


  imin=0,nstlim = 0, !do not run a minimization or MD run

  ntb=2, !constant pressure periodic boundary conditions


  cut=15.0, !8 ang classic bond cutoff


  ifqnt=1 !switch on QM/MM







  qm_ewald = 0 !Use a real-space cutoff for QM-QM and QM-MM long range interactions.



   method = 'B3LYP',

   basis = '6-31G* Freq'



Note: I added Freq to the basis line because I want Gaussian to run a frequency calculation rather than a single point energy calculation. I have looked at the Gaussian input file that sander generates and this works as I intended.


My issue is that when I run this code with a particular butanol molecule (say molecule ID 2 in the center), the code runs fine but when I center a different BOH molecule (say molecule 4), I get the error:


ERROR: QM region + cutoff larger than box dimension:

  QM-MM Cutoff = 15.0000

   Coord Lower Upper Size Radius of largest sphere inside unit cell

     X -16.717 16.393 33.110 17.739

     Y -17.607 17.986 35.593 17.739

     Z -16.921 17.314 34.235 17.739


SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>

QM region + cutoff larger than box

cannot continue, need larger box.


It’s really strange because the box size in both cases doesn’t change and the QM region should be almost exactly the same because in both cases it is one butanol molecule. Since my box dimensions are ~35 angstoms each, I thought a cutoff of 15 was more than adequate but that doesn’t seem to be the case. I have attached here my inpcrd and output files for case 1 (files ending in 2.inpcrd and 2.out) with BOH2 (works) and case 2 (files ending in 4.inpcrd and 4.out) with BOH 4 (doesn’t work).


If anyone can share any insight as to why this is happening or a general rule of thumb on selecting cutoffs, I would very much appreciate it.


Thank you very much,


Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University

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Received on Mon Oct 24 2016 - 12:30:04 PDT
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