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AMBER Archive (2006)Subject: AMBER: puzzles about solvatoct or solvatebox
From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
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:
solvatebox system TIP3PBOX 8:
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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