nmropt is not just for NMR related things. it's for weight changes and
restraints. so you will need to learn how to turn this on.
it's hard to really know what your file looks like due to pasting in.
compare to working inputs.
is there a title line? are the number of spaces before the lines the same in
both files?
On Mon, Jun 6, 2011 at 10:42 AM, Julian Zachmann <
FrankJulian.Zachmann.uab.cat> wrote:
> Thank you for your response.
> Yes, the other files are working properly. I just ran the minimization with
> them.
>
> I haven't used nmropt because these ligands were just "drawn" and then
> calculated into 3d automatically. So there are no nmr or any other
> restraints.
> However, adding nmropt =1, or nmropt =0.5 didn't change anything. Still the
> ctrl namelist is not found.
>
>
> Here is the input file:
>
> &cntrl
> nstlim=15000, ntt=3, gamma_ln=1000.0
> cut=18.0, ntb=0, vlimit=20
> ntc=1, dielc=10,
> vlimit=10,
> ntb=0, nmropt=0.5
> /
>
> &wt type='TEMP0', istep1=0,istep2=1000,
> value1=0.,value2=1200.,
> /
> &wt type='TEMP0', istep1=1001, istep2=3000,
> value1=1200.,value2=1200.0,
> /
> &wt type='TEMP0', istep1=3001, istep2=15000,
> value1=1200.,value2=0.0,
> /
> Could not find cntrl namelist
>
>
> 2011/6/6 Carlos Simmerling <carlos.simmerling.gmail.com>
>
> > do the existing inputs (test suite) work fine? If yes, it's best to try
> to
> > change your inputs stepwise to match a working one.
> >
> > NOTE THAT YOUR TEMPERATURE CHANGES WILL NOT WORK AS YOU WROTE THEM. you
> > need
> > to use the nmropt variable for the %wt sections to be read- look into the
> > tutorials on the amber page.
> >
> > On Mon, Jun 6, 2011 at 10:24 AM, Julian Zachmann <
> > FrankJulian.Zachmann.uab.cat> wrote:
> >
> > > Dear Users.
> > >
> > > I am trying to run Simulated Annealing to minimize ligands that I have
> > > downloaded from a database. "Normal" minimization was not successful as
> > it
> > > brought me only to the closest minima but still the ligand conformation
> > is
> > > unrealistic.
> > > I have no restraint and I want to run them in vacuum.
> > >
> > > But I got the mistake:
> > > Could not find cntrl namelist
> > >
> > > What did I do wrong?
> > > This is the first time I am running SA in Amber so I am thankful for
> any
> > > other advises concerning the input file.
> > >
> > > Best Regards,
> > > Julian
> > >
> > > This is the input file that I used:
> > >
> > > &cntrl
> > > nstlim=15000, ntt=3, gamma_ln=1000.0
> > > cut=18.0, ntb=0, vlimit=20
> > > ntc=1, dielc=10,
> > > vlimit=10,
> > > ntb=0,
> > > /
> > >
> > > &wt type='TEMP0', istep1=0,istep2=1000,
> > > value1=0.,value2=1200.,
> > > /
> > > &wt type='TEMP0', istep1=1001, istep2=3000,
> > > value1=1200.,value2=1200.0,
> > > /
> > > &wt type='TEMP0', istep1=3001, istep2=15000,
> > > value1=1200.,value2=0.0,
> > > /
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Mon Jun 06 2011 - 08:00:03 PDT
