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Re: queries

Hi Ahsan,

> 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?

It is very promising. Additionally you may want to check it with Verify3d,
ProsaII or any  other structure evaluation program.

> 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.

inside the MUTATE_MODEL routine in  the PICK_ATOMS command you can additionally
identify the residue positions with SELECTION_SEGMENT. It is true that in the
manual example only the residue type was set but you can further specify
parameters: please look at PICK_ATOMS command for details

> 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?

If your sugar ligand does not have a topological entry  in the toplib files
than you have two choices, either just assume that the ligand will act as a
rigid body upon docking, or create a topology entry. For the second case please
look at the FAQ  17 on pp 111 in the manual.

> PS:How can I join your mailing list?

Look at our web site  at salilab.org

best wishes,


Andras Fiser, PhD            # phone: (212) 327 7206
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras