Hi rose,
I have a script for analysing,
it began with calculating rmsd, followed by measuring rmsf then doing cross correlation and pca analysing.
Is it correct to use the structure from 1 ns (it is not neccessary in the equilibration state).
Thanks
Homa
----- Original Message -----
From: Ross Walker <ross.rosswalker.co.uk>
Date: Tuesday, July 13, 2010 4:55 pm
Subject: Re: [AMBER] reference structure
To: 'AMBER Mailing List' <amber.ambermd.org>
> Hi Homa,
>
> > I use the structure after 1 ns as reference, I have question
> is it
> > correct or I must use the structure of first frame ( at the
> time of
> > starting)?
>
> You can use ANY reference structure you chose. The question is
> what you want
> to measure with respect to. If for example, you are measuring
> some kind of
> fluctuation then it is probably reasonable to pick an equilibrated
> structure. If you want to show RMSD to the crystal structure
> then of course
> you need to pick the original inpcrd created from the pdb file
> as you
> reference structure (and avoid including H's in the RMS fit
> since these are
> normally placed using templates). Etc.
>
> So please describe what you are trying to do and we can comment
> some more.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of
> Chemistry and
> Biochemistry |
> |
> University of California San
> Diego |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Tue Jul 13 2010 - 00:30:03 PDT
