Thank you Sir, I'll check it out.
On Mon, 10 Jul, 2023, 8:59 pm David A Case, <david.case.rutgers.edu> wrote:
> On Mon, Jul 10, 2023, KAJAL ABROL via AMBER wrote:
>
> To add to what Carlos posted:
>
> >
> >While following the tutorial for Crystal simulations in Amber, I am facing
> >difficulty in providing crystallization conditions to the protein
>
> Amber can't help you with this. If you have locations for alcohols or
> other
> cryo-protection agents, you would create unit for these in the same way as
> for any other non-covalent ligand. If you don't know what the contents of
> the solvent are (the usual case) you are probably stuck with assuming that
> any missing material is water.
>
> >I tried this command for minimization (This is the command for implicit
> >solvent):
> >sander -O -i min.in -p solv1AHO.top -c solv1AHO.crd -o min1.out -r
> min1.rst7
> >
> >So, no ".rst" file is generating,
>
> The "-r" flag specifies the restart file, and it is named "min1.rst7". Do
> you have that file? You should certainly study the min1.out file to see
> more about what happened.
>
> Crystal simulations are no different than solution ones in operation. So,
> get comfortable with those first.
>
> ....dac
>
>
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Received on Mon Jul 10 2023 - 10:00:02 PDT
