I think you have a lot of things going on here, and my advice would be to
make sure you're comfortable with building and running standard simulations
in solution before taking this step.
It sounds like you need to know more about building systems, as well as
making custom force field parameters.
You can look here:
http://ambermd.org/tutorials/BuildingSystems.php
http://ambermd.org/tutorials/ForceField.php
The intro tutorials on the Amber site are very good for learning how to set
up a simulation in explicit water. I suggest doing a system with only
standard parameters first.
http://ambermd.org/tutorials/basic/tutorial13/index.php
You can work through that one, and then move on to building any new force
field parameters.
Once your system is working in solution, you can move on to a crystal
lattice simulation.
As you do these, you could let us know of any questions by reference the
exact steps you take, along with the input files and specific error
messages that you encounter. That is much more helpful than the general
questions that you listed below.
On Mon, Jul 10, 2023 at 9:41 AM KAJAL ABROL via AMBER <amber.ambermd.org>
wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 10 2023 - 07:00:02 PDT
