Re: AMBER: Fwd: QM region + cutoff larger that box

From: M. L. Dodson <>
Date: Sat, 04 Aug 2007 09:32:17 -0500

Francesco Pietra wrote:
> Although I suspected the problem does not arise from the box size, I have rerun
> md for the eq conformer. I started from prepin used successfully for the ax
> conformer in chcl3 and for both conformers in h2o. Setting the chloroform box
> 20A and md nstlim = 20,000.
> I have reexamined the and, they seem to be correct.
> It bombed at step 19150 with same indication "QM part + cutoff larger than
> box". As on previous runs, the mdcrd file shows the solute correctly immersed
> in molecules, allegedly chloroform. Say "allegedly" because of what said
> previously (below).
> Thanks
> francesco pietra

Well, I've had a lot of practical experience recently with the
QMMM functionality, so let me give it a try.

You say you did the run similarly to tutorial A2, but what is your
QM region definition? If you just copied the ':1-2' mask value of
the tutorial (first two residues), then the QM region probably
includes one of the solvent molecules. To follow up that
speculation, if that is what you did, then the QM CHCl3 is
diffusing away from the solute, moving out of the box.

If your mask definition is equivalent to ':1' (i.e., just the
solute), then you must have cleaved your solute into two fragments
(not very likely). To get a QM region component to move out of
the QM box, the QM region must start with at least two components.

Please post your input file.

No help here on your VMD problem. My experience with VMD is that
it is very comprehensive and flexible, but you have to tell it
EXACTLY what you want to do if your problem is different from what
the VMD developers had in mind (and put that capability in the
menus). I.e., it is a programming language as much as a graphics

Bud Dodson

> --- Francesco Pietra <> wrote:
>> Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
>> From: Francesco Pietra <>
>> Subject: QM region + cutoff larger that box
>> To: Amber <>
>> QM-MM run successfully (20,000 steps) for axial methylcyclohexane in
>> chloroform
>> along the lines of Tutorial A2 with Amber9.
>> Equatorial methylcyclohexane also run successfully for 10,000 steps. When I
>> attemped to double nstlim (20,000), run bombed because QM region + cutoff
>> (8.0)
>> larger than box (15.0). I repeated the run, instead of two consecutive 10,000
>> steps, just a single run of 20,000 starting from where the 10,000-step run
>> had
>> been successful. Same error bombing. out file for the latter run attached. I
>> can't grasp where my error is.
>> An additional query: I was unable to delete chloroform from VMD. Curiously,
>> if
>> I indicate to show carbon only, this is shown correctly for the
>> methylcyclohexane molecule, while chloroform is shown as an ammonia-like
>> umbrella with four identical atoms. I.e., chlorine is shown as if it were
>> carbon. Should I select a color for chlorine? I was unable to trace where to
>> deal with chlorine atom. I used the chloroform box in Amber9.
>> All that because I am checking convergence for ESCF with a simple test,
>> flexible molecule.
>> Thanks
>> francesco pietra

M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
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Received on Sun Aug 05 2007 - 06:08:08 PDT
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