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 - 08:30:02 PDT
