hi, so what's your specific question here? :D
Hai
On Tue, Dec 20, 2016 at 1:15 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> Hi,
>
> My system consists of a protein-ligand complex with few co-crystallized
> waters and I am trying to add ions to this system.
>
> I am using AmberTool16. First I solvated my system and next when I tried
> 1) addIonsRand: I found that ions were random distributed but some of the
> ions were within my protein. Therefore, I can not use such system.
>
> 2) addions2: I found that all ions were outside the water box and were
> arranged in one plane. I understand that "addions2" considers solute and
> solvent both and therefore added ions were outside the box.
>
> 3) addions: This time I found that ions were within the solvent box and
> were not inside the protein. But, the ions are still not uniformly
> distributed (see attached figure). I am afraid if it may affect my
> simulation.
>
>
>
>
> *Thanks,Hirdesh*
>
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Received on Tue Dec 20 2016 - 10:30:03 PST
