[AMBER] addion issue

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Tue, 20 Dec 2016 12:15:58 -0600


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


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(image/png attachment: ions.png)

Received on Tue Dec 20 2016 - 10:30:03 PST
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