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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Received on Mon Jun 06 2011 - 08:00:02 PDT
