[MMTK] some general questions

Marc Gasser marc.gasser at pharma.ethz.ch
Thu Apr 22 16:00:52 CEST 2004


Hi MMTK users,

As you will realise I'm a novice in this field and I can't
participate the EMBO course next summer, so I try to find
some answers here.

1. 	I wanna simulate a protein-ligand complex by MMTK,
	what kind of charges do you suggest to be assigned
	to the ligand?
	what's wrong with Gasteiger charges on a protein?

2.	how can I add counterions to a universe? is there a
	possibility to play with different pH values and different
	protonation states of the protein or ligand? what about
	tautomerism?

3. 	Is it possible to set positional restraints on a set of
	atoms, and to reduce the restraints during the simulation,
	e.g. the backbone atoms are positionally restrained at the
	beginning of a simulation, all 100 steps the restraints 
	are reduced by some energy value.
	the fixed attribute of atoms is freezing them totally, if I
	understood correctly, isn't it?

4.	What about modeling one or more mutations within a proteinchain
	of a PDB-file, is there a method which is generating coordinates
	for the new aminoacids?

5.	somehow I didn't really understand the term 'configuration' in the
	manual. Is there a difference between 'conformation of a protein'
	and 'configuration of a protein', or is 'configuration'
	all information and 'conformation' information of positions.

6.	this is from a example from the MMTK distribution.
		
		minimizer = SteepestDescentMinimizer(world, step_size = 0.05*Units.Ang)
		minimizer(steps = 100)
	
	what exactly does the second line? I mean it starts the minimization
	but why not something like

		minimizer.minimize(steps=100)

	?

thank you for helpful suggestions

Cheers,
Marc



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