# AMBER Archive (2006)Subject: AMBER: puzzles about solvatoct or solvatebox

From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
Date: Thu Oct 12 2006 - 05:00:08 CDT

Dear All,

I've solvated my system using the command of "solvateoct system TIP3PBOX 8", then I loaded the resulted prmtop and inpcrd files into the VMD to have a look, I found that the solute is not in the center of oct-box, about 3 residues were not in the oct-box at a side, while the opposite side were far away from the solute. The whole system were totally in the oct-box wall untill I used the command of "solvateoct system TIP3PBOX 12", the solute was still not in the oct-box. In fact, I think if the solute was in the center, the buffer value of 8 is enough to solvate it, don't need to use the buffer of 12 with the cost of more 2400 waters. Moreover, "solvatebox system TIP3PBOX 8" can solvate the solute perfectly with a rectangle box. Herein, I have three questions:

1. can I centered the solute in the oct-box so that I only use the buffer of 8? if can, how to do it then?

2. when I checked the "leap.log" file, I found following informations:

solvateoct system TIP3PBOX 8:
Scaling up box by a factor of 1.461295 to meet diagonal cut criterion
Solute vdw bounding box: 55.503 52.480 61.103
Total bounding box for atom centers: 84.483 84.483 84.483
(box expansion for 'iso' is 19.3%)
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 5 y= 5 z= 5
Adding box at: x=0 y=0 z=0
Center of solvent box is: 37.548698, 37.548698, 37.548698
.....

solvatebox system TIP3PBOX 8:
Solute vdw bounding box: 56.079 52.450 60.643
Total bounding box for atom centers: 72.079 68.450 76.643
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 4 y= 4 z= 5
Adding box at: x=0 y=0 z=0
Center of solvent box is: 28.161524, 28.161524, 37.548698
.....

it seems that xleap don't add a big complete box (or octbox) while a series of unit box, is this true? why?

3. In this "solvation" step, are there some principles or experiential rules? such as which type of box is more efficient, which buffer value is suitable or enough? etc...

Any advice will be greatly appreciated! Thanks in advance & Best regards!

yours sincerely, Zhihong Yu

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