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. Thanks asmat salim HEJ Res Inst of Chem Univ of Karachi Pakistan
PS:How can I join your mailing list?
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
participants (2)
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Andras Fiser -
Dr Ahsan Salim