[MMTK] Using MMTK

Matias Saavedra matias_saavedra at yahoo.com
Mon Jul 18 18:33:26 CEST 2005


>Could you make them with a few lines of Python code
directly on the 
>previously minimized structure instead? As soon as
you start from a >PDB 
>file with its limited resolution, all the precision
of previous 
>minimizations are necessarily lost, so to make any
progress you must 
>get around the PDB file limitation.--- khinsen at cea.fr
wrote:

Aha... i don't see clearly how to modify the structure
directly on the minimized file, because i want to make
mutations that change glycine residues into alanin
(thus calculating new carbon coordenates).

But, as time is my principal concern, can i use a
minimized pdb structure to launch again the
minimization, expecting a BIG reduction in calculating
time, compared with the very first minimization?

And if this is possible, how do i extract a PDB like
file from the results of the minimization?

Thanks

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