[MMTK] using MMTK

Matias Saavedra matias_saavedra at yahoo.com
Mon Jul 18 17:46:48 CEST 2005

The rigid units i'm using are the residues.

> Note that for studying active sites, it sounds
> reasonable to have 
> smaller rigid units (if any) around the active sites
> and bigger ones 
> further away.
how can i set diferent rigid units in the same
structure for the same analysis?

> Don't try to save the minimized configuration in a
> PDB file for later 
> reloading: the precision of the positions in a PDB
> file is not enough 
> to describe the minimum well enough that no further
> minimization is 
> necessary.
I get it, but what i'm trying to do is to make some
modifications at the structure of the same protein and
launch again the Normal Modes analysis.... i want to
repeat that step several times, with different small
structural modifications. I make those modifications
directly in the PDB structure. Taking this into
account, my problem is to launch a minimization for
every slightly modified PDB file, because minimization
takes too much time. What can i do in that case?

Thanks  a lot.

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