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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>
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Received on Mon Jun 06 2011 - 07:30:03 PDT
