Hi Brian. Answering to your question, no, there are no broken bonds in the
prmtop.
Here is the entire input:
polyA-polyT 10-mer: 20ps MD with res on DNA
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 8.0,
noshakemask = '',
ntr = 0,
ntc = 2,
ntf = 1,
temp0 = 298.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 1000000, dt = 0.0005, ntave = 100,
ntpr = 100, ntwx = 100, ntwr = 100,
ig = 10703, ioutfm = 1, iwrap = 1,
icfe = 1, ifsc = 1, clambda = 0.04691,
ifqnt = 1, scmask = ':342.H2', idecomp = 1, nmropt = 0,
/
&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=0,
qm_theory='DFTB',
qmshake=1,
qm_ewald=1, qm_pme=1
qmcut=9.0
writepdb=1
/
Receptor residues
RRES 1 7853
END
Printing
RES 1 342
END
END
Hope this helps.
Thank you again
Fabrício
2013/2/20 Brian Radak <radak004.umn.edu>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
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Received on Wed Feb 20 2013 - 11:00:03 PST
