Re: [AMBER] reference structure

From: Ross Walker <>
Date: Mon, 12 Jul 2010 23:54:39 -0700

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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Jul 13 2010 - 00:00:04 PDT
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