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minimization with biosym

Josep Ll. Gelpi gelpi at sgenz.bq.ub.es
Wed Jul 12 14:53:14 EST 1995

szeliasf at chip.ucdavis.edu (Elias Fernandez) wrote:
>i have been trying to minimize a portion of a protein with biosym. i 
>first solvate the entire molecule. i have been trying to include only the 
>solvent molecules in and around the active site in the minimization. i'd 
>like to also run a dynamics on this small portion. however, i haven't 
>been able to include the water molecules around the active site.
>has any one used the biosym-insight/discover software to do this?
>i'd like to know if there was a way here.
>elias fernandez.
I assume what you mean is that you want to keep fixed all the solvent except
that is close to the active site. 

You don't need to solvate all the protein, just a sphere big enough around
what you want to simulate. In all cases, the protocol would be as follows:

a) Make sure that insight has made an assembly (xxxx_all) that includes the
protein and
solvent (It must do it). If not use the associate command to do it.
If you have crystallographic waters in a separate object, use add assembly
to put everything together.
b)Use the interface command to define a subset around the residues you are
interested in. Do it both for the protein and solvent objects.
c)Substract these subsets from the entire protein and solvent. This will give
you the subsets to be fixed in the simulation.
d) From the discover interface, use fix molecule to fix those subsets, and
make sure you start the simulation for the whole assembly (in the run command).

Josep Ll. Gelpi
Dept. Biochemistry & Molecular Biology
Univ. Barcelona

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