AMBER Archive (2007)

Subject: Fwd: Re: AMBER: solvation of protein using TIP3PBOX in amber 8

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Mon Jan 15 2007 - 23:14:12 CST

Syed Tarique Moin <tarisyed_at_yahoo.com> wrote: Date: Sun, 14 Jan 2007 01:59:32 -0800 (PST)
From: Syed Tarique Moin <tarisyed_at_yahoo.com>
Subject: Re: AMBER: solvation of protein using TIP3PBOX in amber 8
To: amber_at_scripps.edu

I used the commands

solvatebox <protein> TIP3PBOX 8.0
edit <protein>

Then the edit window open showing that, the protein is not totally enclosed in the solvent shell, but the same protein is working with amber 7 having WATBOX216 solvent model.

The situation with the commands addions

addions <protein> Na+ 0
edit protein

then the edit window showing that ions are linealy placed at one side of the protein, but in amber 7, it's showing that ions are placed properly showing its proper place of neutralization.

Thanks in advance

 

"David A. Case" <case_at_scripps.edu> wrote: On Sat, Jan 13, 2007, Syed Tarique Moin wrote:
>
> Plz guide me as, during solvation my protein is not fully enclosed in a
> solvent, i.e protein is found to be away from solvent and solvent is
> found at one end or half covered the protein.

First, this sounds like an imaging problem: have you used the image facility
in ptraj to get your protein/water system into a familiar orientation?

If this doesn't help (or you don't understand what I am saying), please give
more details: just saying that this happens "during solvation" is not enough.
We need to know more about what you actually did in order to offer any advice.

...regards....dac

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Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com
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Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com
 
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