Greetings!
While following the tutorial for Crystal simulations in Amber, I am facing
difficulty in providing crystallization conditions to the protein and how
to generate .prp, .frcmod file formats for the simulation and the
preparation of cryo solution and its simulation. In this regard, I would
like to request you to please provide suitable help for Add to Box
utility/cryo solution preparation.
Another doubt is that, for generating minimization, heat, and production md
files, there is no ".rst" file generated in the tutorial folder. Only
".top" (topology file) and ".crd" file is generated. What commands I can
use for generating these md production files, including minimization and
heating.
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, or do I need to use Explicit solvent
commands for crystal simulations. But I am not able to find the exact
commands and scripts for running energy minimization, heating and md
production run.
Please let me know in this regard. It would be really helpful for me.
Thanking You,
With Regards,
Kajal Abrol
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Received on Mon Jul 10 2023 - 07:00:02 PDT
