hello，
I recommend Charmm-gui to you. It is a convenient tool to build your
system with a lot of options.
If you want run command on your own server, PackMol or PackMol-memgen
may help you.
good luck.
On 2023/8/24 3:57, Prithviraj Nandigrami via AMBER wrote:
> Dear AMBER Users and Experts,
>
> I wanted to have your general guidance regarding setting up explicit
> solvent simulations with ions under Periodic Boundary Conditions (PBC). Of
> course, I can add neutralizing ions to make the net system charge zero,
> which will have (say) K+ and Cl- ions added to the system at a certain
> concentration.
>
> On top of this, if I want to add ions at a certain concentration (say, Cl-)
> to the system, is there any issue that I need to be aware of since PBC is
> already implemented?
>
> I would appreciate any help/guidance regarding this.
>
> Best regards,
>
> PN
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Received on Wed Aug 23 2023 - 22:00:02 PDT
