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
>>>
>> _______________________________________________
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>>
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>
--
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
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Received on Mon Jun 06 2011 - 08:00:04 PDT
