Hi again Fabricio,
The first thing that comes to mind is a bit silly and I expect it is not
the problem, but constraints are based on equilibrium values from the
topology; does the unexpectedly broken bond exist in the prmtop? rdparm or
parmed should help you diagnose that pretty quickly.
Can you post the cntrl section of your input too, just for completeness?
I'm not particularly familiar with the softcore code, but the effect on
bonded terms may or may not be different than in the normal TI code. Then
again, the effected atom is not involved in the transformation at all
right, other than through the coupling of the electronic structure?
Perhaps Ross or Thomas will see this and be able to offer more insight.
Regards,
Brian
On Tue, Feb 19, 2013 at 5:32 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> I am struggling with TI calculations using qmmm (DFTB method) for quite
> some time now. I've had all sorts of different problems, but most of them I
> could understand that what the cause was and, either work my way around or
> fix it. Now I came across something I was not expecting to happen. I have
> set my qmshake = 1 and a bond from one of the oxygens of an aspartic acid
> side chain carboxyl group has broken. This residue is not part of my
> softcore group of atoms, so, I believed that shake was actually being
> applied to these atoms. And also, this atom was not supposed to fly around
> (chemically speaking), there is not enough energy to break that bond. Some
> help here would be great.
> Here is the qm part of the input file:
> &qmmm
> qmmask=
> ':200,255,258&!.CA,C,HA,O,N,HN,H|:341,342|(:202,204&!.CA,C,HA,O,N,H)'
> dftb_3rd_order = 'PA'
> qmcharge=-1,
> diag_routine=2,
> qm_theory='DFTB',
> qmshake=1,
> qm_ewald=1, qm_pme=1
> qmcut=9.0
> writepdb=1
>
> The softcore residue is 342 and the aspartic acid is residue 202.
> Thank you
> Fabrício Bracht
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Received on Wed Feb 20 2013 - 06:30:03 PST
