[Chimera-users] Fwd: Combining fragments for RESP charges

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 31 13:51:55 PDT 2008

Hi Francesco,
I will assume this is just a building issue.  If Sirius is doing  
something else such as automatically  adjusting the charges where the  
atoms are being joined, you would have to do that yourself.

Why not just use the original structure that already includes the  
covalently bound residue?

Even though you would have to chop it into pieces for the RESP part,  
if it is just a matter of putting the atoms back together to recreate  
the original structure, instead just use that structure.

If there is no original structure with that group, you can create the  
group attached to the protein using Build Structure in Chimera, the  
Modify Atoms section.

You can put pre-existing multi-atom pieces together with Chimera, but  
it is currently rather inconvenient.  When you create a bond between  
fragments in Chimera, it does not automatically reposition either  
fragment but connects them without changing their positions.  So if  
they weren't already in the correct positions relative to each other,  
you would have to get them in such a position manually.  The next  
issue is that usually you can't move groups of atoms relative to  
others unless they are in two different models, but then you can't  
bond them unless they are in the same model.  If they needed to be  
moved, you would need to open them from separate files (so they would  
be separate models), reposition relative to each other by activating/ 
deactivating and using the mouse,
then put them in the same model, then add the bond with Build  
Structure or the command "bond."
You could put them in the same model by writing out PDB files and text- 
editing to create a single file, or by using the new "combine" command  
or "copy/combine" function in the Model Panel (would need a recent  
daily build for these to be available).

Instead of all this, I would probably just build the group onto the  
protein from scratch using Build Structure, as mentioned above.
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 31, 2008, at 12:36 AM, Francesco Pietra wrote:
> Subject: Combining fragments for RESP charges
> I was reading Ross Walker's tutorial A1, in the suite of tutorials  
> for Amber.
> When deriving RESP charges for an unusual molecule covalently bound to
> a protein, the unusual molecule is first detached from the protein and
> then further divided into fragments. RESP charges are derived for the
> fragments, then the fragments are recombined using Sirius
> visualization program. The recombined fragments are then attached to
> the protein, again using Sirius.
> Can these recombinations be carried out with Chimera?
> Thanks
> francesco pietra

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