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I have been doing structural studies on various eye lens crystallins by
homology modelling using modeller 4. I have some queries in this regard.

1.The final models have no residues in the disallowed region of the
Ramachandaran plot as well as there are no bad contacts. Is this
evaluation enough for structure verification?

2. I want to mutate one residue in these models and I have gone thru the
top files for mutation. For reasons unknown to me, I could not use it
correctly. Besides the file needs the name of the residue to be mutated
and the one to be inserted instead but not the position. If the specific
name is given, all residues of the same name gets mutated.

3. The other important studies that I want to carry out is the effect of
sugar binding to the structure as well as binding of the small molucules
like phosphate, cyanate etc. I used Web lab Viewer Pro version to paste
and connect the small mol. to my protein.When I cleaned the entire
structure using "clean structure" command in Web lab, it leaves so many
bad contacts and many residues in the disallowed region of the
Ramachandaran plot.
So I decided to use the molecular dynamics and energy minimization by
MODELLER. The topology files do not have these small molecules in the
list. So it leaves the structure to be more disturbed.
Can you make the topology files if specified or can you help me sort out
how to make one?
Well these are so many questions! Can you please suggest something.
asmat salim
HEJ Res Inst of Chem
Univ of Karachi

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