Re: [AMBER] stripping water and cross-correlation analysis

From: case <>
Date: Wed, 23 Jun 2010 00:29:07 -0400

On Wed, Jun 23, 2010, Homa Azizian wrote:
> Is it true that for calculating correlation it should be better to strip
> :WAT before?

It should not make any difference.

> I have done to analysis of cross-correlation of C-alpha of protein one
> with previously strip :WAT and the other one without it. the result of
> 2d-plot from cross-correlation in totaly diffrent. I want to know why it
> happed? what is the effect of stripping water on C-alpha?

We need to know what commands you used. If you stripped the waters first,
you would need to construct a new prmtop file (without waters) before
proceeding with the cross-correlation analysis. Also, when you strip waters,
you generally want to use the "nobox" option on the trajout command. But
I'm just guessing here about things that may have gone wrong.

Without knowing a lot more about what you actually did, it's hard to be of
much help.


AMBER mailing list
Received on Tue Jun 22 2010 - 22:00:04 PDT
Custom Search