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