AMBER Archive (2006)

Subject: Re: AMBER: AMBER - leap - problems with impose command

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Dec 16 2006 - 00:22:36 CST

Quoting Piotr Cieplak <cieplak_at_cgl.ucsf.edu>:

> I am having problems with understanding why tleap changes orientation of
> the coordinates of the molecule in space after changing internal
> coordinates by impose command.
> When I have a dimer and do impose on one residue belonging to the first chain
> - then this first chain changes orientation in space destroying the
> whole complex,
> The coordinates of the second chain stay intact.
> The question is - what is the trick to keep the whole complex intact?

I wonder if it is not a normal feature, I mean in LEaP. I might be
wrong but I wonder if the same thing also appends with 2 DNA
strands... It appends also in InsightII (Accelrys Inc). My
understanding of this is that each time you move an atom a part
remains fix and another moves. I guess if you have no chemical bond
between your two chains, it is normal the second one does not move if
you change the 1st one. I think if your 2 chains were bounded it would
be different. What about trying this sequence ?

- load your structure in LEaP
- Create a temporary bond between your 2 chains/change the molecule topology
- do your impose command
- remove the temporary bond created/rebuild the initial topology

regards, Francois

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