[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] where to put the ligand?



Hi all:

   Thanks for Alicia and Modeler taker's kind hlep last time. Here come 
some new questions.
   Basically I just want to build a homology model complexed with an 
additional ligand. This time, I created a small molecule(ethane) to 
test whether the method works.
    First,In InsightII, I built ethane and optimized using cvff ( the 
program did not allow me to use charmm22 at that time.) and output it 
as an RTF file in charmm22 force field.-
    Second, I did some modification to some of the library files:
    1. append part of the content of RTF file to the end of 
top_allh.lib and top_heav.lib
    2. add an  entry to  restyp.lib, use j as the one  letter        
abbreviation.
       (142 | ETH                 | j | ETHL | ethyl )
 
     Third, alignment was modified so that "j' was appended to the end 
of the target sequence and '-' was used in the relative position of the 
template sequence.
     The program worked well with the above changes, but I could not 
see any ligand shown in the created pdb file! I could see heme was 
shown as the 513th residue but no ethane was shown as the 514th residue!
     Here I attached the ali file,wish you can give me some 
suggestions.
     Again, I would like to ask whether it is correct for me to 
just put any ligand at the end of the target sequence in the alignment 
file? Is it necessary to create the restraint file when some ligands 
are introduced? If fact, in the above test, I just want to see the 
ligand 
are really in the final model, and I do not mind where is it? So, 
anyone can tell me how to make the ligand appear in the final model?
  
        
                                                                  youbin


Attachment: 1a1vsc5f.ali
Description: Binary data