Thank you. i shall follow and get back.
On Mon, Nov 24, 2014 at 9:53 PM, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> You may want to increase the frequency of printing, then visualize it in a
> graphical program like VMD to see the structure that is giving you trouble.
>
> Gustavo Seabra.
>
> Em 24/11/2014 10:28, "Ayesha Fatima" <ayeshafatima.69.gmail.com> escreveu:
> >
> > Dear Dr. Seabra,
> > Thank you for the suggestion. i think I came across one of your older
> posts
> > on the mailing list and did use it. however after 100 steps either the
> > convergence failure and then vlimit exceed warning and crash. Is it
> because
> > of the qmshake=0. This is because I expect the hydrogen bonds between
> > ligand and receptor to be broken as already seen in MM. The error exists
> > even at qmshake=1, so cant be because of this.
> >
> > I am referring also to Dubey et al. (J Biol Phys, 2010) paper. they have
> > "applied shake on hydrogen atoms". I cant follow this statement. what
> > parameter to add?
> > I shall be grateful.
> >
> > Thank you
> >
> > On Mon, Nov 24, 2014 at 8:43 PM, Gustavo Seabra <
> gustavo.seabra.gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Have you tried changing the defaul setting for DFTB_TELEC? It's not
> > > something that should be messed with often, but may help in this
> situation.
> > > You may try to set it to 100 just until yiu are over this problem, then
> > > change it back to the default (0).
> > >
> > > Hope that helps,
> > > Gustavo Seabra.
> > > Em 24/11/2014 03:11, "Ayesha Fatima" <ayeshafatima.69.gmail.com>
> escreveu:
> > >
> > > > Dear all,
> > > > I am trying to run a qm/mm on a protein-ligand system. I have
> > > successfully
> > > > done classical MD without errors. As per information on the mailing
> list,
> > > > for qm/mm, i used a well equilibrated .rst file from the classical MM
> > > > method and was able to do further equilibration with qm/mm using the
> PM3
> > > > Hamiltonian. It is in the MD production phase.
> > > > I want to repeat the same with SCC-DFTB but unfortunately it keeps
> giving
> > > > errors in the equilibration phase such as
> > > >
> > > > QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
> > > > QMMM SCC-DFTB: Convergence could not be achieved in this step.
> > > > QMMM SCC-DFTB: The calculation will continue, but energies and
> > > > QMMM SCC-DFTB: forces for this step will not be accurate.
> > > >
> > > > I have looked around on the mailing list and know its a common error.
> I
> > > > also tried using the PM3 equilibrated file and trying to further
> > > > equilibrate it with the SCC-DFTB. But the error still remains. I am
> > > > attaching my input file. I am sure someone has done it and resolved
> the
> > > > issue. Could they share their experience?
> > > > Thank you
> > > > Regards
> > > > Ayesha Fatima
> > > > PhD candidate UM
> > > >
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Received on Mon Nov 24 2014 - 06:00:05 PST
