I mean that the bonds that are broken are not broken in the prmtop.
Sorry for any confusion.
Fabrício
2013/2/20 Brian Radak <radak004.umn.edu>
> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > 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
> > > 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.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > 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
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 20 2013 - 14:00:03 PST
