Hi, Julian,
I didn't see a title line in your input file. The "&cntrl" line must be the
second line in the input file. If this is the problem or not, please study
the tutorials carefully, as instructed by the previous recommendations by
the Amber masters earlier in the thread.
HTH,
kevin
On Mon, Jun 6, 2011 at 10:45 AM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Dear Julian
>
> Please look at the tutorials and the manual
>
> nmropt=0.5 is meaningless, and these days nmropt=1 can be used for many
> more things than nmr restraints. nmropt=1 enables the reading of the
> namelist below.
>
> Adrian
>
>
> On 6/6/11 4:42 PM, Julian Zachmann 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,
> >>> /
> >>> _______________________________________________
> >>> 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
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- - -
HK
-------------------------------------------------------
Kevin Eduard Hauser
National Science Foundation,
LSAMP Bridge to the Doctorate Fellow
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
Phone: (561) 635.1848
Email: 84hauser.gmail.com
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Received on Mon Jun 06 2011 - 10:30:04 PDT
