AMBER Archive (2007)

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

From: David A. Case (case_at_scripps.edu)
Date: Sat Jan 13 2007 - 23:40:46 CST

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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