[MMTK] some general questions
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
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
thank you for helpful suggestions
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