Do you mean "no, the bonds that are broken are not in the prmtop" or "no,
the bonds that are broken are not broken in the prmtop"?
On Wed, Feb 20, 2013 at 1:56 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> 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
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> > >
> >
> >
> >
> > --
> > ================================ 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
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
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> appropriate
> > address.
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--
================================ 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
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Feb 20 2013 - 11:30:03 PST
