Re: [AMBER] upper limit of water with solvateBox

From: Ikuo KURISAKI <>
Date: Thu, 22 Mar 2018 09:54:18 +0900

Dear Dr. Mashaly, Prof. Case,

I'd appreciate your kind replies.
Using octahedral box sounds one good option,
Although I still need to add > 100k water.
Then I will try AddToBox.

Yours sincerely,


-----Original Message-----
From: Ahmed Mashaly []
Sent: Wednesday, March 21, 2018 11:07 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] upper limit of water with solvateBox

I have had a similar problem, this error was not reproducible with Dan.

And yes I noticed that it happened with water +100 K molecule.Finally, we decided to go for an octahedral box with less amount of water, hope you can find another answer.
 Kind Regards,Ahmed

      From: Ikuo KURISAKI <>
 To: 'AMBER Mailing List' <>
 Sent: Wednesday, March 21, 2018 2:06 PM
 Subject: [AMBER] upper limit of water with solvateBox
Dear Ambers,


Thank you for usual support.

I have a question for upper limit of solvent number

when we use solvatebox command of tLEaP.


I tried to add > 100000 molecules to protein system, which give ca 300000 atoms

By executing "solvateBox UNIT TIP3P 54".

However, water molecules were not properly arranged in solvation box,

Where the 'box' is not rectangular, rather have convex portion on the rectangular.


This problem does not appear for smaller number of water molecules, i.e.

In my case.

Amber14 and 16 were employed, but both of them show the same results.


I'm most glad if you give any advice for this point.


Best regards,



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Received on Wed Mar 21 2018 - 18:00:02 PDT
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